Improve Python Example use_case_02.py with additional example codes #423

mhitzem · 2021-08-11T15:53:26Z

Generates a new csv file with random data (fake scalar data)
Data from file is read and put into uint32 and float32 arrays and added to AttributeMatrix and DataContainer

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

* Replace malloc/free with new/delete[] * Reintroduce SimpleITKExplicit library to solve symbol loading issues on macOS. * Fix allocation errors in DataArray and StructArray Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

…zSoftware#376) * Updates to codes to expose double precision versions where needed * MatrixMath is now mostly templated to work on any POD. * Fix return type in MatrixMath and remove spurious newline in ImportHDF5Dataset * More Fixes and Updates to Quaternion related classes. Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

…rtzSoftware#379) Copying a DataContainerReader filter to the clipboard in SVPipelineView no longer copies the entire pipeline that was written instead. This is done by taking advantage of JsonFilterParametersWriter::setExpandReaderFilters(bool) to avoid modifying behavior used to write DREAM.3D files. Signed-off-by: Matthew Marine <matthew.marine@bluequartz.net>

* Added const to appropriate DataArray functions * NeighborList::writeH5Data needed some additional changes since it was trying to modify a member variable * Added const to appropriate Geometry functions * LinkedDataContainerSelectionWidget needed the IGeometry include to work * Added const to DynamicTableData::getTableData() * Added const to appropriate functions in AM, DC, and DCA classes

…changes Methods exposed to Python bindings that were changed to be a "const" method needed to have the CONST_METHOD argument added to the macro. Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

…sues commit 4166131 Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Wed Oct 30 14:52:10 2019 -0400 Fix bug using std::accumulate due to casting issue. Passing in "1" will force the computation to be done in int32_t. When using large Tuple dimensions we will over flow. Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> commit b216f5a Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Tue Oct 29 17:05:05 2019 -0400 Add missing include directive <memory> for shared_ptr<> access. Updated some other code areas with better documentation strings Updated some code sections to be more consistent with use of type aliases. Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> commit d16dc31 Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Tue Oct 29 13:37:16 2019 -0400 Update codes to latest const correctness changes Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> commit 643d99b Merge: f5958ad c055656 Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Tue Oct 29 09:11:37 2019 -0400 Fix compiler errors due to PYBIND_11 macros not being updated to API changes * develop: Fix compiler errors due to PYBIND_11 macros not being updated to API changes Feature/const (BlueQuartzSoftware#380) # Conflicts: # Source/SIMPLib/DataArrays/StatsDataArray.h # Source/SIMPLib/DataArrays/StringDataArray.h # Source/SIMPLib/DataContainers/AttributeMatrix.h # Source/SIMPLib/DataContainers/DataContainerArray.h # Source/SIMPLib/Geometry/IGeometry.h # Source/SIMPLib/Geometry/IGeometry2D.h # Source/SIMPLib/Geometry/IGeometryGrid.h # Source/SIMPLib/Geometry/ImageGeom.h # Source/SVWidgetsLib/FilterParameterWidgets/LinkedDataContainerSelectionWidget.cpp commit f5958ad Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Mon Oct 28 13:37:21 2019 -0400 Feature/const (BlueQuartzSoftware#380) * Added const to appropriate DataArray functions * NeighborList::writeH5Data needed some additional changes since it was trying to modify a member variable * Added const to appropriate Geometry functions * LinkedDataContainerSelectionWidget needed the IGeometry include to work * Added const to DynamicTableData::getTableData() * Added const to appropriate functions in AM, DC, and DCA classes Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> commit 4cb6eec Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Fri Oct 25 15:18:25 2019 -0400 Address feedback from code review. Remove static const from constants.h Fix duplicate variable names in experimental file. commit a292511 Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Fri Oct 25 12:35:24 2019 -0400 Add conditional #pragma for clang diagnostics Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> commit 6f73a64 Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Fri Oct 25 12:12:57 2019 -0400 Fixing compiler errors on MSVC Platform Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> commit 316d395 Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Fri Oct 25 11:53:57 2019 -0400 Fix DOxygen comments that got munged up in some find/replace operation Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> commit 693c2fe Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Fri Oct 25 11:43:17 2019 -0400 Fix compiler warnings about overriding a virtual method without using override keyword Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> commit 7775443 Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Thu Oct 24 12:40:33 2019 -0400 Improve generated CPP code to modern standards Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> commit 4a50ac7 Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Thu Oct 24 12:40:14 2019 -0400 Add a clang pragma to quiet a warning about using std::move. Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> commit ad86eb0 Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Thu Oct 24 09:24:09 2019 -0400 Update Messages classes and remove Python Wrapping from pure virtual class Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> commit 051a664 Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Wed Oct 23 14:42:52 2019 -0400 Fix warnings about returning const QString as a value instead of a reference. Warnings are fixed by changing from "const QString" to "QString" Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> commit 66bf335 Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Wed Oct 23 14:03:47 2019 -0400 Merge and Compile error fixes Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> commit 4536233 Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Thu Jun 27 18:02:45 2019 -0400 Fix more pass by reference for POD types Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> commit 3fb6d31 Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Thu Jun 27 10:49:58 2019 -0400 Resolving merge conflicts Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> commit 8e6826d Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Mon Jun 24 18:06:26 2019 -0400 Fixing code based on feed back from PR Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> commit 3995ead Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Fri Jun 21 14:24:15 2019 -0400 Fix pass by const reference for POD types In the last pass at removing the macros POD types were mistakenly passed by const reference instead of by value. These have all been fixed to pass by value. Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> commit 71df37a Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Thu Jun 13 18:14:59 2019 -0400 Massive code modifications to clean up and reduce macro clutter * Remove use of all SIMPL_* macros replacing with actual C++ code * Remove the include directive to DataContainerArray in AbstractFilter instead using a forward declaration and alias * Add needed include directives or forward declarations to all effected classes Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> commit f6ba40d Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Thu Jun 13 18:57:23 2019 -0400 Transfer some SIMPL_* macros into the Pybind11 macro section This is needed because the codescraper algorithm looks for four specific macros in order to determine the proper c++ and python code to generate. The same macros have been defined in the SIMPLPythonMacros.h header file. Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> commit 35b2d0e Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Tue Jun 11 18:19:16 2019 -0400 Wrap the Python wrapping macros in a #define for SIMPL_ENABLE_PYTHON This is done because SIMPLibSetGetMacros is going away eventually and we need to separate out the still needed macros that help generate the python bindings. Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> commit ca158c3 Author: Michael Jackson <mike.jackson@bluequartz.net> Date: Tue Jun 11 18:05:43 2019 -0400 Add compiler define if SIMPL_ENABLE_PYTHON is turned on. Update clang-format to NOT sort the includes. Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net> Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

* Default constructor still expands reader filters. * The constructor accepting filename, pipeline name, and number of filters once again does not expand reader filters. Booleans default construct to false. Signed-off-by: Matthew Marine <matthew.marine@bluequartz.net>

…lueQuartzSoftware#378) * Add filter that generates a tilt series of images from an ImageGeom * Creating Unit test that only tests the basic functionality A deeper unit test that has exemplar output images needs to be created. * Address use of static const. updates BlueQuartzSoftware#378 * Added check to prevent accessing unallocated array elements * GenerateTiltSeries::generateGrid() could try to create a grid coordinates array with 0 elements and then access it depending on the user input for the spacing. * Changed the axis constants in GenerateTiltSeries to be static constexpr * Add another array to the debugged vertex array that stores the FeatureIds. This allows the developer to more easily debug the rotated geometries complete with the proper data. * Added parameter for the prefix of the output data containers * Changed constants to be constexpr * Ran clang-format * Update codes to latest API Changes. * Adjusted some debugging data arrays that get created. * Rewrite Grid generation be specific for X, Y or Z Axis. The generic versions were to difficult and obtuse to get working. * Added test for GenerateTiltSeries filter * Compares against GenerateTiltSeriesTest.dream3d from DREAM3D_Data repo * Added copyright notice * Ran clang-format Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

…eneration (BlueQuartzSoftware#383) Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

* Fix compile bug on gcc where sqrtf isn't in std namespace * For gcc, sqrtf is not in the std namespace but sqrt is * Fixed compile bug for gcc with static constexpr variable

These were meant for debugging only but may be used in a future version as a user option Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

* m_InitValue is now set to the initValue parameter instead of static_cast<T>(0) Signed-off-by: Matthew Marine <matthew.marine@bluequartz.net>

…f strings (BlueQuartzSoftware#384) * Added static function for creating a Requirement with a vector of strings * Changed usage of QVector<AttributeMatrix::Type> to AttributeMatrix::Types

This change removes compiler warnings about redeclaring some of the macros. In order to truly fix the issue the developers would need to understand that there is an exact order when including <math.h> or <cmath>. With this change we can just include SIMPLibMath.h and not have to worry about the proper include order Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Signed-off-by: Joey Kleingers <joey.kleingers@bluequartz.net>

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Signed-off-by: Joey Kleingers <joey.kleingers@bluequartz.net>

…generated." This reverts commit fc766d5.

* Moved RotateSampleRefFrame filter to SIMPL Core Filters * Fixed include error * Fixed compile error for GCC * Fix Python binding compile error * Updated copyright info * Add missing include directives (strictly) Cleanup warnings on change of precision casts. Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

…rame

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

…d of QMetaProperty (BlueQuartzSoftware#386) * Update Filter Parameter Widgets to use std::function callbacks instead of QMetaProperty Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

…re#387) Explicitly instantiating each variation of DataArray<T> This should cut down on compile times (somewhat). Add MarkDown as supported InfoStringFormat for DataArray<> Fixing some typos in the Float Comparison Macros Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

* CreateGeometry uses uint64 arrays for Edge List, Triangle List, etc. * datacheck() searched for uint64 arrays, but the GUI only allowed the user to input int64 arrays

…ersion 1.4 Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Signed-off-by: Jared Duffey <jared.duffey@bluequartz.net>

* Declaring all bound classes before adding methods allows the right name to be used in docstrings Signed-off-by: Jared Duffey <jared.duffey@bluequartz.net>

The data arrays that were set for things such as the vertex shared list were not being removed from the source Attribute Matrix when the user selected to have the data MOVED instead of COPIED. Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Check for &, :, / or \ as those characters can cause issues down the road when written to disk. Minor include cleanup via removing headers that are not needed. Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Signed-off-by: Jared Duffey <jared.duffey@bluequartz.net>

What we found out today: You can call a member function of a null pointer as long as the function never dereferences 'this'. Now we know. Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

…ten. Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

…e text Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Signed-off-by: Jared Duffey <jared.duffey@bluequartz.net>

* Improves python docstrings * More type safe for C++ side Signed-off-by: Jared Duffey <jared.duffey@bluequartz.net>

* Casting functions would create a python object and then immediately destroy it upon return. Future accesses would then cause a crash * Improved some of the generated docstrings for typecasters * Changed assert to static_assert for QChar size * Added several new type casters to cover previously unconvertable types * Fixed some type conversion issues for unbound sub types Signed-off-by: Jared Duffey <jared.duffey@bluequartz.net>

* Allows for split declaration/definition before the macro based bindings * Added several more bound types Signed-off-by: Jared Duffey <jared.duffey@bluequartz.net>

* Uses mypy stubgen Signed-off-by: Jared Duffey <jared.duffey@bluequartz.net>

imikejackson

Also, could we also add an argument "--output_dir" to the main args that allows the user to set where all of the output files are created. Be sure to flow that through all needed parts of the code.

Wrapping/Python/Examples/use_case_02.py

imikejackson · 2021-08-11T19:19:26Z

Wrapping/Python/Examples/use_case_02.py

+
+    #Creates arrays from data with shape of (# of vertices x 1)
+    uintarr = np.ndarray(shape=(37989, 1), dtype=np.uint32, buffer=uints)
+    floatarr = np.ndarray(shape=(37989, 1), dtype=np.float32, buffer=f32s)


use the numVerts variable from above instead of the 37989 hard coded value.

Wrapping/Python/Examples/use_case_02.py

imikejackson · 2021-08-12T16:40:16Z

Wrapping/Python/Examples/use_case_02.py

+
+    # Add AttributeMatirx to DataContainer
+    dc.addOrReplaceAttributeMatrix(am)



See if you can add the DREAM3D filter "apply_transformation_to_geometry" which is in the DREAM3DReview plugin. Take a look at https://github.com/dream3d/DREAM3DReview/blob/develop/Test/Python/Apply_Transformation_To_Geometry.py file for inspiration.

In that example we are using a transformation matrix but see if you can figure out how to use just a scaling factor in each direction. Try out a scaling factor of 10x in each direction just to make it obvious when the data is viewed.

Write out the dream3d file before the transformation and after then use ParaView to view the results and verify that you have successfully scaled the vertices.

imikejackson and others added 30 commits August 26, 2019 10:17

Correct issue with static cast on Linux.

5bb1fe6

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Update/fix formatting inside ImportHDF5 Data set documentation

ec3980c

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Fix compiler error due to missing macro definition

b0dff13

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Fix compiler errors due to PYBIND_11 macros not being updated to API …

c055656

…changes Methods exposed to Python bindings that were changed to be a "const" method needed to have the CONST_METHOD argument added to the macro. Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Add include directive to ensure that ITK_v5CONST is properly defined.

12cfa13

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Allow user to set the start, stop and increment for the tilt series g…

a29be09

…eneration (BlueQuartzSoftware#383) Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Feature/generate tilt series fix (BlueQuartzSoftware#382)

799983b

* Fix compile bug on gcc where sqrtf isn't in std namespace * For gcc, sqrtf is not in the std namespace but sqrt is * Fixed compile bug for gcc with static constexpr variable

Remove Debug Data Containers that get generated.

bad4728

These were meant for debugging only but may be used in a future version as a user option Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Fixed DataArray constructor not using initValue parameter

5654242

* m_InitValue is now set to the initValue parameter instead of static_cast<T>(0) Signed-off-by: Matthew Marine <matthew.marine@bluequartz.net>

Add DataArraySelectionFilterParameter::CreateRequirement for vector o…

f8a8e2c

…f strings (BlueQuartzSoftware#384) * Added static function for creating a Requirement with a vector of strings * Changed usage of QVector<AttributeMatrix::Type> to AttributeMatrix::Types

Convert FileListInfo into a superclass with subclasses.

14d1dda

Signed-off-by: Joey Kleingers <joey.kleingers@bluequartz.net>

Fixing compile errors and test failures.

31c25ab

Signed-off-by: Joey Kleingers <joey.kleingers@bluequartz.net>

Fix alias to use a const where appropriate

1c28c20

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Montage file lists with one row and/or one column can now be generated.

fc766d5

Signed-off-by: Joey Kleingers <joey.kleingers@bluequartz.net>

Declaring DataContainerArray::Pointer as a Qt metatype.

cdbc044

Signed-off-by: Joey Kleingers <joey.kleingers@bluequartz.net>

Revert "Montage file lists with one row and/or one column can now be …

641c371

…generated." This reverts commit fc766d5.

Fixed bug where the wrong property name was used for RotateSampleRefF…

b2a046f

…rame

Add MarkDown to InfoStringFormat

9aa77d5

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Update Filter Parameter Widgets to use std::function callbacks instea…

6911da6

…d of QMetaProperty (BlueQuartzSoftware#386) * Update Filter Parameter Widgets to use std::function callbacks instead of QMetaProperty Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Fixed filter parameter requirement for CreateGeometry filter

424185e

* CreateGeometry uses uint64 arrays for Edge List, Triangle List, etc. * datacheck() searched for uint64 arrays, but the GUI only allowed the user to input int64 arrays

imikejackson and others added 19 commits April 27, 2021 17:28

Update ghcFileSystem find_package() NAMES for updated ghfFileSystem v…

18920c0

…ersion 1.4 Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Fixed PYB11_METHOD args that led to bad docstrings being generated

4a0ab8d

Signed-off-by: Jared Duffey <jared.duffey@bluequartz.net>

Changed Python binding generation to forward declare classes

a60857c

* Declaring all bound classes before adding methods allows the right name to be used in docstrings Signed-off-by: Jared Duffey <jared.duffey@bluequartz.net>

NeighborLists are not written to XDMF Files as they serve no purpose.

56f35a7

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Remove unused variable from neighborlist

7e46d03

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Added simpl_helpers to dream3d conda package

3756530

Signed-off-by: Jared Duffey <jared.duffey@bluequartz.net>

Fix unexpected null pointer warning filter drag leave event.

86b74a1

What we found out today: You can call a member function of a null pointer as long as the function never dereferences 'this'. Now we know. Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Started document that has ideas of python examples that could be writ…

653ce8a

…ten. Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Adding more example python ideas

357f3a6

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Adding example python codes that show creating Geometries from scratch

0296ffb

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

OCD got the best of me. Had to fix the spelling mistake in the licens…

ea01af1

…e text Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>

Added more python __repr__ functions for data structure items

8b9287c

Signed-off-by: Jared Duffey <jared.duffey@bluequartz.net>

Changed Create functions to use specific types instead of QVariant

83a0980

* Improves python docstrings * More type safe for C++ side Signed-off-by: Jared Duffey <jared.duffey@bluequartz.net>

Added new code location in generated python binding

4e509ff

* Allows for split declaration/definition before the macro based bindings * Added several more bound types Signed-off-by: Jared Duffey <jared.duffey@bluequartz.net>

Added option to generate python stub files (.pyi)

416f767

* Uses mypy stubgen Signed-off-by: Jared Duffey <jared.duffey@bluequartz.net>

Update use_case_02.py

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imikejackson reviewed Aug 11, 2021

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Update use_case_02.py

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imikejackson changed the title ~~Adding scalar data to XYZ coordinate~~ Improve Python Example use_case_02.py with additional example codes Aug 12, 2021

imikejackson assigned mhitzem Aug 12, 2021

imikejackson added Enhancement Code added that makes life easier good first issue labels Aug 12, 2021

imikejackson reviewed Aug 12, 2021

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Update use_case_02.py

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imikejackson force-pushed the develop branch from 39e6c89 to f6a579a Compare April 26, 2023 17:26

imikejackson force-pushed the develop branch from 1db029e to f45085c Compare October 26, 2024 20:36

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Improve Python Example use_case_02.py with additional example codes #423

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		# Add AttributeMatirx to DataContainer
		dc.addOrReplaceAttributeMatrix(am)

Improve Python Example use_case_02.py with additional example codes #423

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