Feature: Add an option to control the discretization of colormap #1678

gapry · 2024-10-25T10:16:57Z

Related Issue:

This work addresses the Issue: #228

Current Progress

Over the past two weeks, I have made significant progress on #228, with my work available for review in the following commits:

These commits introduce a new CLI option and extend the vtkF3DRenderer class to handle this option.

Please note that the PR isn’t fully complete yet, as it does not fully resolve #228. I will continue to work on it to ensure that all aspects are addressed.

Since I’ve already spent two weeks on this task, I wanted to report my progress, especially as we’re working remotely.

Next Steps

I will review the VTK documentation to learn how to adjust color settings, specifically focusing on the vtkDiscretizableColorTransferFunction.

mwestphal · 2024-10-25T10:18:24Z

library/options.json

@@ -246,6 +246,10 @@
        "type": "double_vector",
        "default_value": "0.0, 0.0, 0.0, 0.0, 0.4, 0.9, 0.0, 0.0, 0.8, 0.9, 0.9, 0.0, 1.0, 1.0, 1.0, 1.0"
      },
+      "discretization" : {
+        "type": "bool",


This option definitely should not be a bool but an int I think.

codecov · 2024-10-25T10:26:34Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 96.90%. Comparing base (caa99fc) to head (9f9a2e9).
Report is 3 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1678   +/-   ##
=======================================
  Coverage   96.90%   96.90%           
=======================================
  Files         105      105           
  Lines        8629     8634    +5     
=======================================
+ Hits         8362     8367    +5     
  Misses        267      267

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mwestphal · 2024-11-01T11:07:35Z

@gapry any news on this ?

gapry · 2024-11-08T00:41:01Z

Dear @mwestphal, I apologize for the delayed response. Here is my current progress:

Part 1 - VTK

I have learned some VTK examples from the official document, https://examples.vtk.org/site/Cxx/. I have chosen the Cube example as a starting point to learn the VTK API and successfully compile and execute in my Ubuntu. The experiment code is host here, https://github.com/gapry/code-for-blog/tree/main/2024/VTK_Cube. Next, I will learn how to use vtkDiscretizableColorTransferFunction to change to Cube.

Also, I have spent the time to read the book, https://book.vtk.org/en/latest/ to learn VTK knowledge

Part 2 - F3D API

According to the document of https://github.com/f3d-app/f3d/tree/master/examples, I need to use the flag Df3d_DIR with the value /path/to/f3d/install/lib/cmake/f3d, but I find it doesn't exist in the f3d directory in the path f3d/install/lib/cmake/

Here is the step to reproduce the issue

cd Workspaces

mkdir f3d
cd f3d

git clone https://github.com/f3d-app/f3d src

mkdir -p build install

cd build
cmake -GNinja -DCMAKE_PREFIX_PATH=../vtk/install -DCMAKE_INSTALL_PREFIX=../install ../src
ninja
ninja install

cd ..

ls -al install/lib
total 1800
drwxrwxr-x 2 gapry gapry    4096 Nov  8 06:26 .
drwxrwxr-x 5 gapry gapry    4096 Nov  8 06:26 ..
lrwxrwxrwx 1 gapry gapry      11 Nov  8 06:26 libf3d.so -> libf3d.so.2
lrwxrwxrwx 1 gapry gapry      13 Nov  8 06:26 libf3d.so.2 -> libf3d.so.2.5
-rw-r--r-- 1 gapry gapry 1745760 Nov  8 06:26 libf3d.so.2.5
-rw-r--r-- 1 gapry gapry   83800 Nov  8 06:26 libvtkext.so

As you can see, it just has some *.so files

So, I decided to try to use cmake -Df3d_DIR:PATH=~/Workspaces/f3d/build/cmake to compile,
it occurs the following error

CMake Error at /home/gapry/Workspaces/f3d/build/cmake/f3dConfig.cmake:93 (message):
  library was requested but could not be found,
  /home/gapry/Workspaces/f3d/build/cmake/library-config.cmake is missing,
  please check component was installed
Call Stack (most recent call first):
  CMakeLists.txt:7 (find_package)

The experiment code is host here, https://github.com/gapry/code-for-blog/tree/main/2024/F3D_RenderImage, you can see I use cmake -Df3d_DIR:PATH=~/Workspaces/f3d/build/cmake .. in the Makefile, https://github.com/gapry/code-for-blog/blob/2b8ace13462c68dc6a7f0e3b1b6645199a8a489d/2024/F3D_RenderImage/Makefile#L14

Do I miss some important thing?

mwestphal · 2024-11-08T06:09:42Z

You need to install the SDK:

cmake --install . --component sdk

from: https://f3d.app/doc/dev/BUILD.html

but you do not need really to build the libf3d examples to do this :)

gapry · 2024-11-09T22:32:31Z

@mwestphal

Thank you for your help, I can see in the f3d directory in the path f3d/install/lib/cmake/,
and update the -Df3d_DIR:PATH in my Makefile.

But it appears another issue I can't solve,

When I use mkdir build; cd build; cmake -Df3d_DIR:PATH=~/Workspaces/f3d/install/lib/cmake/f3d ..; make to compile one of libf3d examples, the code is here, it occurs the following error, https://gist.github.com/gapry/b5cdf79d3c5f52bf32e3c0aa06fbb51a

And I do the following checking:

check the libf3d.so.2.5, and I make sure it exists

$ file /home/gapry/Workspaces/f3d/install/lib/libf3d.so.2.5
/home/gapry/Workspaces/f3d/install/lib/libf3d.so.2.5: ELF 64-bit LSB shared object, x86-64, version 1 (GNU/Linux), dynamically linked, BuildID[sha1]=324b457d94b4427c8817e986c72cc9722c1b0efe, not stripped

read the document again, according to the overview, I make sure I have turned on the macro BUILD_SHARED_LIBS during compiling the libf3d, here is the full step

$ cd Workspaces

$ mkdir f3d
$ cd f3d

$ git clone https://github.com/f3d-app/f3d src

$ mkdir -p build install

$ cd build
$ cmake -GNinja -DCMAKE_PREFIX_PATH=../vtk/install -DCMAKE_INSTALL_PREFIX=../install -DBUILD_SHARED_LIBS=ON ../src
$ cmake --install . --component sdk
$ ninja
$ ninja install

$ cd ../
$ ls install
bin  include  lib  share
$ ls install/lib
cmake  libf3d.so  libf3d.so.2  libf3d.so.2.5  libvtkext.so

Am I missing something important, doing something wrong?

gapry · 2024-11-09T22:40:43Z

@mwestphal

I know I can add some unit tests for the new features, but I find VTK have a lot of examples, https://examples.vtk.org/site/Cxx/, to help the new developers, so I think I can do similar things, write a new example application for libf3d.

Just want to share my thoughts to you.

mwestphal · 2024-11-17T12:23:03Z

Hi @gapry

Do you need any help moving forward with this ?

mwestphal · 2024-11-24T06:34:51Z

Hi @gapry

Do you need any help moving forward with this ?

gapry · 2024-11-24T06:49:24Z

@mwestphal I sincerely apologize for my delayed response.

Question:

According to the document, Gallery, I find the colormap can be variadic, like void simple_printf(const char* fmt, ...), e.g.

$ f3d backpack.vti -vmn --range=300,1000 --colormap=0,0,0,0,1,1,1,1
$ f3d single-pin.vtp -xtbgans --range=-2,8 --colormap=0,0.3,0.7,0,0.7,0,0.1,1,1,0.8,0.8,0
$ f3d pointCloud.vtp -o --point-size=0.2 --colormap=0,0,0.8,0,0.4,0.9,0,0,0.8,0.9,0.9,0,1,0.5,0.5,1 --up=+Z

so, I don't know how to define the type. e.g. vector<RGB>, vector<RGBA>, ... , etc ???

According to the document, Final shaders, I don't how to pass the colormap to the fragment shader.

mwestphal · 2024-11-24T07:11:18Z

so, I don't know how to define the type. e.g. vector, vector, ... , etc ???

What do you mean ? You do not need to define a new type. You can just change the discretization of the colormap in the vtkF3DRenderer in ConfigureRangeAndCTFForColoring by using the VTK method: vtkDiscretizableColorTransferFunction::SetNumberOfValues
https://vtk.org/doc/nightly/html/classvtkDiscretizableColorTransferFunction.html#add05ecb2a72eeaec91588366fa7ea64d

gapry · 2024-11-24T07:34:06Z

According to the document, Gallery, I find the colormap the usage as following

First Usage

$ f3d backpack.vti -vmn --range=300,1000 --colormap=0,0,0,0,1,1,1,1

I can get two RGBA groups

0, 0, 0, 0
1, 1, 1, 1

Second Usage

$ f3d single-pin.vtp -xtbgans --range=-2,8 --colormap=0,0.3,0.7,0,0.7,0,0.1,1,1,0.8,0.8,0

I can get three RGBA groups

0,   0.3, 0.7, 0
0.7,   0, 0.1, 1
1,   0.8, 0.8, 0

Third Usage

$ f3d pointCloud.vtp -o --point-size=0.2 --colormap=0,0,0.8,0,0.4,0.9,0,0,0.8,0.9,0.9,0,1,0.5,0.5,1 --up=+Z

I can get four RGBA groups

  0,   0, 0.8, 0, 
0.4, 0.9,   0, 0, 
0.8, 0.9, 0.9, 0, 
  1, 0.5, 0.5, 1

So, I think the colormap is used RGBA as unit, but according to the https://github.com/f3d-app/f3d/blob/master/vtkext/private/module/vtkF3DRenderer.cxx#L2548

void vtkF3DRenderer::ConfigureRangeAndCTFForColoring(
  const F3DColoringInfoHandler::ColoringInfo& info)
{
...
  for (size_t i = 0; i < this->Colormap.size(); i += 4)
  {
    double val = this->Colormap[i];
    double r = this->Colormap[i + 1];
    double g = this->Colormap[i + 2];
    double b = this->Colormap[i + 3];
    this->ColorTransferFunction->AddRGBPoint(
      this->ColorRange[0] + val * (this->ColorRange[1] - this->ColorRange[0]), r, g, b);
  }
...
}

It appears the colormap is decomposed into val, r, g, b, rather than r, g, b, a. This is causing some confusion for me. For now, I still don't understand the purpose of double val = this->Colormap[i];

mwestphal · 2024-11-24T07:45:20Z

From https://f3d.app/doc/user/OPTIONS.html

Set a custom colormap for the coloring.
This is a list of colors in the format val1,red1,green1,blue1,...,valN,redN,greenN,blueN
where all values are in the range (0,1).
Ignored if --colormap-file option is specified.
Use with the scalar option.

Opacity is never mentioned. There are four values because the first value is the scalar value.

VAL R G B

gapry · 2024-11-24T07:55:11Z

@mwestphal Thank you! I understand now. I apologize for not reading the documentation carefully. I will use vtkDiscretizableColorTransferFunction::SetNumberOfValue, https://vtk.org/doc/nightly/html/classvtkDiscretizableColorTransferFunction.html#add05ecb2a72eeaec91588366fa7ea64d, to continue the work.

gapry · 2024-11-30T07:00:54Z

Current Progress

I pushed the new commits and the following screenshots are my testing results.

The key changes

set the default value of discretization is 256
in vtkF3DRenderer::SetColorDiscretization(const int discretization), I use
vtkF3DMetaImporter::ColoringInfo info to call
this->ConfigureRangeAndCTFForColoring(info);
in ConfigureRangeAndCTFForColoring, call the
vtkDiscretizableColorTransferFunction::SetNumberOfValue

Test Case 1: don't use the option`--colormap-discretization`

./build/bin/f3d assets/f3d-data/dragon.vtu -xtganse --comp=0 \
  --colormap=1.0,255.0,127.0,63.0

Result

Test Case 2: set `--colormap-discretization=25600`

./build/bin/f3d assets/f3d-data/dragon.vtu -xtganse --comp=0 \
  --colormap-discretization=25600 --colormap=1.0,255.0,127.0,63.0

Result

Test Case 3: set `--colormap-discretization=64`

./build/bin/f3d assets/f3d-data/dragon.vtu -xtganse --comp=0 \
  --colormap-discretization=64 --colormap=1.0,255.0,127.0,63.0

Result

Conclusion

Unfortunately, this confirms that my implementation is incorrect.

snoyer · 2024-11-30T07:33:11Z

Unfortunately, this confirms that my implementation is incorrect.

--colormap=1.0,255.0,127.0,63.0 will give you a colormap with a single color regardless of your implementation tho. Maybe your implementation works but you just can't tell?

Try --colormap=0,1,0,0,1,0,0,1 to map value 0 to red and 1 to blue

mwestphal reviewed Oct 25, 2024

View reviewed changes

gapry force-pushed the issue-228 branch from e2f3f56 to f8bbaac Compare November 29, 2024 14:31

gapry added 5 commits November 30, 2024 15:05

Add CLI option to discretize colormap

249321f

[PoC][Part02]: Add CLI option to discretize colormap

4899fc1

change option type from bool to vector<double>

68a0dbc

change option type from vector<double> to int

5df8019

fix: the default value of discretization is 256

dd9c2b8

gapry force-pushed the issue-228 branch from 2eaa062 to dd9c2b8 Compare November 30, 2024 07:12

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Feature: Add an option to control the discretization of colormap #1678

Feature: Add an option to control the discretization of colormap #1678

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Feature: Add an option to control the discretization of colormap #1678

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Feature: Add an option to control the discretization of colormap #1678

Conversation

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Related Issue:

Current Progress

Next Steps

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Codecov Report

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Part 1 - VTK

Part 2 - F3D API

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First Usage

Second Usage

Third Usage

mwestphal commented Nov 24, 2024

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Current Progress

The key changes

Test Case 1: don't use the option--colormap-discretization

Test Case 2: set --colormap-discretization=25600

Test Case 3: set --colormap-discretization=64

Conclusion

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Test Case 1: don't use the option`--colormap-discretization`

Test Case 2: set `--colormap-discretization=25600`

Test Case 3: set `--colormap-discretization=64`