Improve Python Example use_case_02.py with additional example codes #423
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mhitzem
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Aug 11, 2021
mhitzem
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- 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 <[email protected]>
Signed-off-by: Michael Jackson <[email protected]>
* 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 <[email protected]>
Signed-off-by: Michael Jackson <[email protected]>
…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 <[email protected]>
…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 <[email protected]>
* 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 <[email protected]>
…sues
commit 4166131
Author: Michael Jackson <[email protected]>
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 <[email protected]>
commit b216f5a
Author: Michael Jackson <[email protected]>
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 <[email protected]>
commit d16dc31
Author: Michael Jackson <[email protected]>
Date: Tue Oct 29 13:37:16 2019 -0400
Update codes to latest const correctness changes
Signed-off-by: Michael Jackson <[email protected]>
commit 643d99b
Merge: f5958ad c055656
Author: Michael Jackson <[email protected]>
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 <[email protected]>
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 <[email protected]>
commit 4cb6eec
Author: Michael Jackson <[email protected]>
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 <[email protected]>
Date: Fri Oct 25 12:35:24 2019 -0400
Add conditional #pragma for clang diagnostics
Signed-off-by: Michael Jackson <[email protected]>
commit 6f73a64
Author: Michael Jackson <[email protected]>
Date: Fri Oct 25 12:12:57 2019 -0400
Fixing compiler errors on MSVC Platform
Signed-off-by: Michael Jackson <[email protected]>
commit 316d395
Author: Michael Jackson <[email protected]>
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 <[email protected]>
commit 693c2fe
Author: Michael Jackson <[email protected]>
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 <[email protected]>
commit 7775443
Author: Michael Jackson <[email protected]>
Date: Thu Oct 24 12:40:33 2019 -0400
Improve generated CPP code to modern standards
Signed-off-by: Michael Jackson <[email protected]>
commit 4a50ac7
Author: Michael Jackson <[email protected]>
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 <[email protected]>
commit ad86eb0
Author: Michael Jackson <[email protected]>
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 <[email protected]>
commit 051a664
Author: Michael Jackson <[email protected]>
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 <[email protected]>
commit 66bf335
Author: Michael Jackson <[email protected]>
Date: Wed Oct 23 14:03:47 2019 -0400
Merge and Compile error fixes
Signed-off-by: Michael Jackson <[email protected]>
commit 4536233
Author: Michael Jackson <[email protected]>
Date: Thu Jun 27 18:02:45 2019 -0400
Fix more pass by reference for POD types
Signed-off-by: Michael Jackson <[email protected]>
commit 3fb6d31
Author: Michael Jackson <[email protected]>
Date: Thu Jun 27 10:49:58 2019 -0400
Resolving merge conflicts
Signed-off-by: Michael Jackson <[email protected]>
commit 8e6826d
Author: Michael Jackson <[email protected]>
Date: Mon Jun 24 18:06:26 2019 -0400
Fixing code based on feed back from PR
Signed-off-by: Michael Jackson <[email protected]>
commit 3995ead
Author: Michael Jackson <[email protected]>
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 <[email protected]>
commit 71df37a
Author: Michael Jackson <[email protected]>
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 <[email protected]>
commit f6ba40d
Author: Michael Jackson <[email protected]>
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 <[email protected]>
commit 35b2d0e
Author: Michael Jackson <[email protected]>
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 <[email protected]>
commit ca158c3
Author: Michael Jackson <[email protected]>
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 <[email protected]>
Signed-off-by: Michael Jackson <[email protected]>
Signed-off-by: Michael Jackson <[email protected]>
* 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 <[email protected]>
…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 <[email protected]>
…eneration (BlueQuartzSoftware#383) Signed-off-by: Michael Jackson <[email protected]>
* 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 <[email protected]>
* m_InitValue is now set to the initValue parameter instead of static_cast<T>(0) Signed-off-by: Matthew Marine <[email protected]>
…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 <[email protected]>
Signed-off-by: Joey Kleingers <[email protected]>
Signed-off-by: Joey Kleingers <[email protected]>
Signed-off-by: Michael Jackson <[email protected]>
Signed-off-by: Joey Kleingers <[email protected]>
Signed-off-by: Joey Kleingers <[email protected]>
…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 <[email protected]>
Signed-off-by: Michael Jackson <[email protected]>
…d of QMetaProperty (BlueQuartzSoftware#386) * Update Filter Parameter Widgets to use std::function callbacks instead of QMetaProperty Signed-off-by: Michael Jackson <[email protected]>
…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 <[email protected]>
* 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
Signed-off-by: Jared Duffey <[email protected]>
* Declaring all bound classes before adding methods allows the right name to be used in docstrings Signed-off-by: Jared Duffey <[email protected]>
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 <[email protected]>
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 <[email protected]>
Signed-off-by: Michael Jackson <[email protected]>
Signed-off-by: Michael Jackson <[email protected]>
Signed-off-by: Jared Duffey <[email protected]>
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 <[email protected]>
…ten. Signed-off-by: Michael Jackson <[email protected]>
Signed-off-by: Michael Jackson <[email protected]>
Signed-off-by: Michael Jackson <[email protected]>
…e text Signed-off-by: Michael Jackson <[email protected]>
Signed-off-by: Jared Duffey <[email protected]>
* Improves python docstrings * More type safe for C++ side Signed-off-by: Jared Duffey <[email protected]>
* 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 <[email protected]>
* Allows for split declaration/definition before the macro based bindings * Added several more bound types Signed-off-by: Jared Duffey <[email protected]>
* Uses mypy stubgen Signed-off-by: Jared Duffey <[email protected]>
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| #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) |
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use the numVerts variable from above instead of the 37989 hard coded value.
imikejackson
changed the title
imikejackson
added
Enhancement
| am.addOrReplaceAttributeArray(f32arr) | ||
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| # Add AttributeMatirx to DataContainer | ||
| dc.addOrReplaceAttributeMatrix(am) | ||
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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.
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