Batch 5: 15 geometry creation/manipulation filter docs reviewed

Tier 2 (8 filters): CreateGeometry, ApplyTransformationToGeometry,
RotateSampleRefFrame, ResampleImageGeom, ResampleRectGridToImageGeom,
PadImageGeometry, QuickSurfaceMesh, InitializeImageGeomCellData.

Tier 3 (7 filters): CreateImageGeometry, CombineTransformationMatrices,
SetImageGeomOriginScaling, CropImageGeometry, AppendImageGeometry,
PartitionGeometry, ComputeCoordinatesImageGeom.

Each rewrite applied the established conventions: Required Input Sources
section naming upstream producers, MyST cross-reference links, explicit
units on numeric parameters, no duplication of the auto-generated
parameter table.

Notable structural changes:
- CreateGeometry: trimmed and reorganized; promoted geometry-type
  taxonomy to a navigable table.
- ApplyTransformationToGeometry: removed duplicate transformation-type
  listing; added explicit cross-reference to CombineTransformationMatrices.
- RotateSampleRefFrame: prominent verified-only-for-axis-aligned banner;
  explicit distinction from ApplyTransformation.
- QuickSurfaceMesh: deprecation banner promoted with explicit
  recommendation to use Surface Nets.
- CropImageGeometry: documented voxels-vs-physical-bounds parameter
  explicitly.
- PadImageGeometry: expanded Default Value semantics and Update Origin
  behavior.

Build verified clean (no new Sphinx warnings).

Author: imikejackson

docs/documentation_review_tracker.md

@@ -14,7 +14,7 @@
 | 2 | Alignment Filters | 5 | 5 | 5 | Complete |
 | 3 | Segmentation / Feature Identification | 10 | 10 | 10 | Complete |
 | 4 | Neighbor / Kernel Operations | 11 | 11 | 11 | Complete |
-| 5 | Geometry Creation / Manipulation | 15 | 15 | 0 | Triaged |
+| 5 | Geometry Creation / Manipulation | 15 | 15 | 15 | Complete |
 | 6 | Data Manipulation (Copy, Create, Delete, Rename) | ~20 | 0 | 0 | Not Started |
 | 7 | I/O Filters (Read/Write) | ~15 | 0 | 0 | Not Started |
 | 8 | Image Processing (ITK wrappers) | ~88 | 0 | 0 | Not Started |
@@ -266,16 +266,16 @@ None. No filter in this batch has a non-expert blocker.
 
 | Filter | Plugin | Status |
 |--------|--------|--------|
-| CreateGeometry | SimplnxCore | Pending |
-| ApplyTransformationToGeometry | SimplnxCore | Pending |
-| RotateSampleRefFrame | SimplnxCore | Pending |
-| ResampleImageGeom | SimplnxCore | Pending |
-| ResampleRectGridToImageGeom | SimplnxCore | Pending |
-| PadImageGeometry | SimplnxCore | Pending |
-| QuickSurfaceMesh | SimplnxCore | Pending |
-| InitializeImageGeomCellData | SimplnxCore | Pending |
-
-- [ ] **CreateGeometryFilter** (SimplnxCore)
+| CreateGeometry | SimplnxCore | Done |
+| ApplyTransformationToGeometry | SimplnxCore | Done |
+| RotateSampleRefFrame | SimplnxCore | Done |
+| ResampleImageGeom | SimplnxCore | Done |
+| ResampleRectGridToImageGeom | SimplnxCore | Done |
+| PadImageGeometry | SimplnxCore | Done |
+| QuickSurfaceMesh | SimplnxCore | Done |
+| InitializeImageGeomCellData | SimplnxCore | Done |
+
+- [x] **CreateGeometryFilter** (SimplnxCore)
   - **Clarity:** Comprehensive but very long (~19KB); the 8-geometry-type taxonomy is buried in dense prose.
   - **Completeness:** Excellent — covers all 8 geometry types with examples, including a complete worked example for importing from text files. Possibly too much for a single filter doc.
   - **Accessibility:** Heavy DREAM3D-NX terminology assumed (Element, Attribute Matrix, shared vertex list).
@@ -285,7 +285,7 @@ None. No filter in this batch has a non-expert blocker.
   - **Concept Links:** Geometry types, Element type, shared vertex list, winding/right-hand rule, Attribute Matrix
   - **Notes:** "DREAM3D Review (Geometry)" group is unusual — verify this is intended. Typo "dimenionality" appears multiple times. Each geometry-type section duplicates content from per-type filters. Consider promoting the geometry-type taxonomy into a shared concept page and trimming this doc to filter-specific guidance.
 
-- [ ] **ApplyTransformationToGeometryFilter** (SimplnxCore)
+- [x] **ApplyTransformationToGeometryFilter** (SimplnxCore)
   - **Clarity:** Strong before/after image sequences explaining the successive-rotation artifact problem. Excellent caveat.
   - **Completeness:** Has duplicate transformation-type listing (bullets at lines 96-103 and the same content as a table at lines 107-114). One needs to go.
   - **Accessibility:** Node vs Image distinction is critical and well-explained; row-major matrix encoding explained.
@@ -295,7 +295,7 @@ None. No filter in this batch has a non-expert blocker.
   - **Concept Links:** transformation matrix, axis-angle, row-major matrix order, interpolation modes
   - **Notes:** Remove the duplicated transformation-type listing. Convert "[Combine Transformation Matrices](CombineTransformationMatricesFilter.md)" link to a proper MyST link (already is). Add Required Input Sources. The relative `./Filter.md` should be checked — current uses both `./` and bare forms.
 
-- [ ] **RotateSampleRefFrameFilter** (SimplnxCore)
+- [x] **RotateSampleRefFrameFilter** (SimplnxCore)
   - **Clarity:** Verified-only-for-axis-aligned-90/180 warning is at the top — good. Distinction from ApplyTransformation (sample reference frame vs geometric rotation) is not made explicit.
   - **Completeness:** Has rotation matrix equivalent shown. Note about origin shift after rotation is valuable.
   - **Accessibility:** "Sample reference frame" jargon assumed; the term needs first-use definition.
@@ -305,7 +305,7 @@ None. No filter in this batch has a non-expert blocker.
   - **Concept Links:** sample reference frame, EBSD frame convention, axis-angle rotation
   - **Notes:** Add explicit "When to Use vs ApplyTransformation" guidance. Make verified-axis-only banner more prominent. Cross-link to SetImageGeomOriginScaling for the origin reset workflow. Add Required Input Sources.
 
-- [ ] **ResampleImageGeomFilter** (SimplnxCore)
+- [x] **ResampleImageGeomFilter** (SimplnxCore)
   - **Clarity:** Three resampling modes (Spacing, Scaling, Exact Dimensions) each with worked numerical examples. Clear.
   - **Completeness:** "No interpolation, closest cell wins" behavior noted. Renumber Features + NeighborList removal warning present.
   - **Accessibility:** Spacing/dimensions/scaling distinction depends on understanding Image Geometry.
@@ -315,7 +315,7 @@ None. No filter in this batch has a non-expert blocker.
   - **Concept Links:** spacing vs scaling vs dimensions, closest-cell resampling, Feature renumbering
   - **Notes:** Cross-link to ApplyTransformation is present but uses `./` path; convert to plain MyST form. Add explicit units callouts per mode. Add Required Input Sources.
 
-- [ ] **ResampleRectGridToImageGeomFilter** (SimplnxCore)
+- [x] **ResampleRectGridToImageGeomFilter** (SimplnxCore)
   - **Clarity:** Brief, just describes the "last one wins" rule.
   - **Completeness:** Missing: when to use this, how to specify the target image geometry's spacing/dimensions, what happens when target is finer than source.
   - **Accessibility:** Rectilinear Grid concept not introduced.
@@ -325,7 +325,7 @@ None. No filter in this batch has a non-expert blocker.
   - **Concept Links:** Rectilinear Grid vs Image Geometry, downsampling vs upsampling
   - **Notes:** Add "When to Use" section. Explain why "last one wins" was chosen (interpolation is wrong for label data). Add Required Input Sources.
 
-- [ ] **PadImageGeometryFilter** (SimplnxCore)
+- [x] **PadImageGeometryFilter** (SimplnxCore)
   - **Clarity:** Very brief; the figures are helpful but the prose underdocuments the "default padding value" semantics.
   - **Completeness:** Doesn't explain what the *Update Origin* option does or when to use it.
   - **Accessibility:** "Default padding value" is undefined.
@@ -335,7 +335,7 @@ None. No filter in this batch has a non-expert blocker.
   - **Concept Links:** padding, image extension, origin shift
   - **Notes:** Expand "default padding value" to "Each padded cell is initialized to the user-specified Default Value, which is interpreted in the same units as each cell-level array being padded". Document *Update Origin* and *Update Spacing* options. Add Required Input Sources.
 
-- [ ] **QuickSurfaceMeshFilter** (SimplnxCore)
+- [x] **QuickSurfaceMeshFilter** (SimplnxCore)
   - **Clarity:** Deprecation notice at top recommending "Surface Nets". Node Types table is excellent. Triangle-pair-per-cell-face algorithm explained.
   - **Completeness:** Has good images for each Node Type. The Verify Triangle Winding reference is implicit; needs a link.
   - **Accessibility:** "Stair stepped" surface mesh result not pictured directly.
@@ -344,7 +344,7 @@ None. No filter in this batch has a non-expert blocker.
   - **Concept Links:** voxel-face-to-triangle conversion, Node Types, FaceLabels convention, mesh windings
   - **Notes:** Improve deprecation banner — make clear when to use this vs Surface Nets. Convert "see Verify Triangle Winding documentation" to a MyST link. Add Required Input Sources (FeatureIds from a segment filter).
 
-- [ ] **InitializeImageGeomCellDataFilter** (SimplnxCore)
+- [x] **InitializeImageGeomCellDataFilter** (SimplnxCore)
   - **Clarity:** Three modes (Manual, Random, Random With Range) are listed but the "subvolume" parameter is undefined.
   - **Completeness:** Missing: how is the subvolume specified (min/max cell indices? physical bounds?). What data types support each random mode? What about boolean arrays?
   - **Accessibility:** Reader has to guess the subvolume specification UI.
@@ -358,15 +358,15 @@ None. No filter in this batch has a non-expert blocker.
 
 | Filter | Plugin | Status |
 |--------|--------|--------|
-| CreateImageGeometry | SimplnxCore | Pending |
-| CombineTransformationMatrices | SimplnxCore | Pending |
-| SetImageGeomOriginScaling | SimplnxCore | Pending |
-| CropImageGeometry | SimplnxCore | Pending |
-| AppendImageGeometry | SimplnxCore | Pending |
-| PartitionGeometry | SimplnxCore | Pending |
-| ComputeCoordinatesImageGeom | SimplnxCore | Pending |
-
-- [ ] **CreateImageGeometryFilter** (SimplnxCore)
+| CreateImageGeometry | SimplnxCore | Done |
+| CombineTransformationMatrices | SimplnxCore | Done |
+| SetImageGeomOriginScaling | SimplnxCore | Done |
+| CropImageGeometry | SimplnxCore | Done |
+| AppendImageGeometry | SimplnxCore | Done |
+| PartitionGeometry | SimplnxCore | Done |
+| ComputeCoordinatesImageGeom | SimplnxCore | Done |
+
+- [x] **CreateImageGeometryFilter** (SimplnxCore)
   - **Clarity:** Deprecation banner is right under the title but as a level-2 heading, making it look like its own section. Confusing.
   - **Completeness:** Dimensions/Spacing/Origin definitions are good.
   - **Accessibility:** Same dense terminology as CreateGeometry.
@@ -376,7 +376,7 @@ None. No filter in this batch has a non-expert blocker.
   - **Concept Links:** Image Geometry dimensions/origin/spacing
   - **Notes:** Move deprecation notice into a clear callout. Fix "dimenionality" typo. Cross-link to CreateGeometry filter. Add Required Input Sources note (none — geometry is created from user parameters).
 
-- [ ] **CombineTransformationMatricesFilter** (SimplnxCore)
+- [x] **CombineTransformationMatricesFilter** (SimplnxCore)
   - **Clarity:** Brief and adequate. Output format documented.
   - **Completeness:** Missing motivating context for why you'd combine matrices (the answer is in ApplyTransformation — referenced indirectly there).
   - **Accessibility:** Assumes user knows row-major 4x4 convention.
@@ -386,7 +386,7 @@ None. No filter in this batch has a non-expert blocker.
   - **Concept Links:** matrix composition, transformation order, row-major matrix order
   - **Notes:** Add a short "Why Use This Filter" pointing to ApplyTransformationToGeometry's caveat about successive image-geometry transformations. Note that matrices are applied left-to-right in the order listed. Add Required Input Sources.
 
-- [ ] **SetImageGeomOriginScalingFilter** (SimplnxCore)
+- [x] **SetImageGeomOriginScalingFilter** (SimplnxCore)
   - **Clarity:** Title says "Set Origin & Spacing" but body only describes the origin parameters. Spacing is implicit.
   - **Completeness:** "Put Input Origin at the Center of Geometry" option mentioned but not explained in detail.
   - **Accessibility:** OK for the limited content provided.
@@ -396,7 +396,7 @@ None. No filter in this batch has a non-expert blocker.
   - **Concept Links:** Image Geometry origin, spacing
   - **Notes:** Document both Origin and Spacing parameter sets. Document the linkable parameters (only-change-origin, only-change-spacing options). Expand the "Put Origin at Center" explanation. Add Required Input Sources.
 
-- [ ] **CropImageGeometryFilter** (SimplnxCore)
+- [x] **CropImageGeometryFilter** (SimplnxCore)
   - **Clarity:** Three worked examples with images. Inclusive-bounds note is critical and called out.
   - **Completeness:** Voxels-vs-physical-coordinates mode is implicit; the "Use Physical Bounds" parameter should be stated explicitly.
   - **Accessibility:** Voxel index 0-based convention is implied via examples.
@@ -406,7 +406,7 @@ None. No filter in this batch has a non-expert blocker.
   - **Concept Links:** ROI cropping, inclusive bounds, voxel indexing
   - **Notes:** Add explicit "Bounds Mode" subsection naming the parameter that toggles voxels vs physical. State units per mode. Update NeighborList warning to use the standard pattern shared with RequireMinimumSizeFeatures.
 
-- [ ] **AppendImageGeometryFilter** (SimplnxCore)
+- [x] **AppendImageGeometryFilter** (SimplnxCore)
   - **Clarity:** Exhaustive examples for X/Y/Z directions with figures.
   - **Completeness:** "Resolution" terminology used in one place — should be "Spacing" per the modern simplnx convention.
   - **Accessibility:** Good.
@@ -416,7 +416,7 @@ None. No filter in this batch has a non-expert blocker.
   - **Concept Links:** geometry concatenation, mirroring, spacing check
   - **Notes:** Replace remaining "Resolution" with "Spacing" for consistency. Cross-link to CreateImageGeometry for the geometry-definition concepts. Add Required Input Sources.
 
-- [ ] **PartitionGeometryFilter** (SimplnxCore)
+- [x] **PartitionGeometryFilter** (SimplnxCore)
   - **Clarity:** Four modes with excellent visual examples and walk-throughs.
   - **Completeness:** "Reconstruction (Reconstruction)" group/subgroup is a stutter — verify.
   - **Accessibility:** Long doc but well-organized with figures.
@@ -426,7 +426,7 @@ None. No filter in this batch has a non-expert blocker.
   - **Concept Links:** spatial partitioning, partition grid, out-of-bounds handling, vertex mask
   - **Notes:** Verify group "Reconstruction (Reconstruction)". Add a short lead-in explaining why partition (spatial analysis, sub-volume statistics, parallel processing prep). Add Required Input Sources.
 
-- [ ] **ComputeCoordinatesImageGeomFilter** (SimplnxCore)
+- [x] **ComputeCoordinatesImageGeomFilter** (SimplnxCore)
   - **Clarity:** "Implicit vs explicit" framing is jargon; the example output is clear.
   - **Completeness:** Three output modes documented with raster scheme.
   - **Accessibility:** Reader benefits from concrete example, which is provided.

src/Plugins/SimplnxCore/docs/AppendImageGeometryFilter.md

@@ -6,8 +6,9 @@ Sampling (Memory/Management)
 
 ## Description
 
-This filter allows the user to append one or multiple image geometries to a given image geometry, in any direction (X,Y,Z). The input and
-destination **ImageGeometry** objects must have the same dimensions in the directions that are NOT chosen.  If the X direction is chosen, the geometries must match in Y & Z.  If the Y direction is chosen, the geometries must match in X & Z.  If the Z direction is chosen, the geometries must match in X & Y.  Optional checks for equal **Resolution** values can also be performed.
+This **Filter** appends one or more **Image Geometries** to a destination Image Geometry along a chosen axis (X, Y, or Z), producing a single larger Image Geometry. The input geometries must have matching dimensions in the two axes that are *not* the append direction. Optionally, the filter can also verify that the input and destination geometries have matching spacing on all axes before appending.
+
+For an introduction to Image Geometry dimensions and spacing, see [Create Image Geometry](CreateImageGeometryFilter.md).
 
 This filter also has an option to mirror the resulting geometry in the chosen direction.  If the X direction is chosen, it will mirror the positions of the YZ planes.  If the Y direction is chosen, it will mirror the positions of the XZ planes.  If the Z direction is chosen, it will mirror the positions of the XY planes.
 
@@ -94,6 +95,10 @@ And here is what the geometry looks like after appending the three pieces togeth
 | ![](Images/AppendImageGeometry/z_complete.png) | ![](Images/AppendImageGeometry/z_mirrored.png) |
 |:----------------------:|:----------------------:|
 
+### Required Input Sources
+
+- **Destination Image Geometry** and **Input Image Geometries** -- all geometries to be appended. Typically produced by [Create Image Geometry](CreateImageGeometryFilter.md), [ITK Import Image Stack](../ITKImageProcessing/ITKImportImageStackFilter.md), or an EBSD reader. All must share matching cell-level Attribute Array names if cell data is to be preserved during the append.
+
 % Auto generated parameter table will be inserted here
 
 ## Example Pipelines