Code Coverage Issues

# Code Coverage Improvement TODO

Generated from GCOV coverage report (Jan 30 2025).
Overall: **38.9% line**, **43.9% function**, **24.5% branch** coverage.

> **Excludes:** `parameterVersion()` and `clone()` (covered by separate PR),
> `IdentifySampleFilter` (already fixed), `not_used/` algorithm stubs.

---

## 1. Algorithm Classes with 0% Coverage (Not Tested At All)

These are **real algorithm implementations** with zero test coverage. Each needs a
corresponding unit test that exercises the algorithm's `operator()()` through its
parent filter.

### OrientationAnalysis Plugin

| File | Lines | Comment |
|------|------|--------------|
| `Filters/Algorithms/ComputeGBPDMetricBased.cpp` | 739 | Times out |
| `Filters/Algorithms/ComputeGBCDMetricBased.cpp` | 612 | Times out |
| `Filters/Algorithms/ComputeGBCD.cpp` | 479 | Times out |
| `Filters/Algorithms/ComputeTwinBoundaries.cpp` | 398 |Times out |
| `Filters/Algorithms/ComputeGBCDPoleFigure.cpp` | 335 | Times out |
| `Filters/Algorithms/ComputeFZQuaternions.cpp` | 180 | Unit test is being run MAJ. Not sure what it is or is not covering |

### SimplnxCore Plugin

| File | Lines | Action |
|------|------:|--------|
| `Filters/Algorithms/ReadDeformKeyFileV12.cpp` | 840 | Add unit test for ReadDeformKeyFileV12Filter |
| `Filters/Algorithms/RegularGridSampleSurfaceMesh.cpp` | 283 | Add unit test for RegularGridSampleSurfaceMeshFilter |
| `Filters/Algorithms/WriteVtkStructuredPoints.cpp` | 74 | Add unit test for WriteVtkStructuredPointsFilter |
| `Filters/Algorithms/ComputeDifferencesMap.cpp` | 61 | Add unit test for ComputeDifferencesMapFilter |

### Near-Zero Coverage

| File | Lines | Coverage | Action |
|------|------:|----------|--------|
| `Filters/Algorithms/ComputeArrayStatistics.cpp` | 1,288 | 9.5% | Expand unit test to exercise more code paths |

### Core Utility

| File | Lines | Action |
|------|------:|--------|
| `simplnx/Utilities/ParallelData2DAlgorithm.cpp` | 39 | Add or expand test that uses 2D parallel algorithm |

---

## 2. Uncovered `MakeErrorResult()` Preflight Branches — Update Unit Tests

These are error-return branches in `preflightImpl()` that are never triggered by
any unit test. For each, add a test case that passes invalid inputs to trigger the
error path. Grouped by filter with line numbers and error codes.

### AddBadDataFilter (4 uncovered)

- [ ] L116 (`-76234`): No noise type selected — pass `boundaryNoise=false, poissonNoise=false`
- [ ] L121 (`-76235`): Poisson volume fraction out of range — pass value > 1.0 or < 0.0
- [ ] L126 (`-76236`): Boundary volume fraction out of range — pass value > 1.0 or < 0.0
- [ ] L133 (`-76237`): Image geometry with null cell Attribute Matrix

### AlignGeometriesFilter (1 uncovered)

- [ ] L83 (`-1`): Invalid alignment type — pass value other than 0 or 1

### ApplyTransformationToGeometryFilter (4 uncovered preflight + 4 other)

- [ ] L173 (`-82000`): Null input geometry
- [ ] L206 (`-82010`): Invalid precomputed transformation matrix path
- [ ] L224 (`-82002`): Manual transformation matrix without exactly 4 rows
- [ ] L228 (`-82006`): Manual transformation matrix without exactly 4 columns

### ApproximatePointCloudHullFilter (1 uncovered)

- [ ] L89 (`-11001`): Grid resolution with zero or negative values

### BadDataNeighborOrientationCheckFilter (9 uncovered)

- [ ] L120: Missing image geometry
- [ ] L127: Missing mask array
- [ ] L133: Mask array with != 1 component
- [ ] L141: Missing cell phases array
- [ ] L151: Cell phases array with != 1 component (not Int32)
- [ ] L159: Missing crystal structures array
- [ ] L169: Crystal structures array with != 1 component (not UInt32)
- [ ] L176: Missing quaternions array
- [ ] L186: Quaternion array with != 4 components (not Float32)

### CAxisSegmentFeaturesFilter (4 uncovered)

- [ ] L131 (`-655`): Misorientation tolerance == 0
- [ ] L157: Missing mask array
- [ ] L162: Mask array wrong type (not Bool or UInt8)
- [ ] L170 (`-651`): DataArrays with unequal tuple counts

### ChangeAngleRepresentationFilter (1 uncovered)

- [ ] L122 (`-67001`): Conversion type > 1

### ComputeArrayHistogramFilter (2 uncovered)

- [ ] L154 (`-57206`): Mask array not Boolean or UInt8
- [ ] L163 (`-57207`): Mask/input array tuple count mismatch

### ComputeArrayHistogramByFeatureFilter (2 uncovered)

- [ ] L154 (`-57206`): Mask array not Boolean or UInt8
- [ ] L163 (`-57207`): Mask/input array tuple count mismatch

### ComputeAvgCAxesFilter (1 uncovered)

- [ ] L102 (`-6400`): DataArrays with unequal tuple counts

### ComputeAvgOrientationsFilter (5 uncovered)

- [ ] L117: Crystal structures array with != 1 component
- [ ] L126: Quaternion array with != 4 components
- [ ] L134: Phases array with != 1 component
- [ ] L142: FeatureIds array with != 1 component
- [ ] L150 (`-651`): DataArrays with unequal tuple counts

### ComputeBiasedFeaturesFilter (1 uncovered)

- [ ] L111 (`-7460`): DataArrays with unequal tuple counts

### ComputeCAxisLocationsFilter (1 uncovered)

- [ ] L95 (`-3520`): DataArrays with unequal tuple counts

### ComputeDifferencesMapFilter (6 uncovered)

- [ ] L38 (`-90001`): Selected arrays of different types
- [ ] L44 (`-90002`): Selected DataPath not pointing to a DataArray
- [ ] L149: Missing first input array
- [ ] L158: Missing second input array
- [ ] L181: First input array wrong number of components
- [ ] L189: Second input array wrong number of components

### ComputeFeatureClusteringFilter (4 uncovered)

- [ ] L127 (`-14310`): Number of bins <= 0
- [ ] L135 (`-14311`): FeaturePhases wrong type
- [ ] L141 (`-14312`): Centroids wrong type
- [ ] L151 (`-14314`): DataArrays with unequal tuple counts

### ComputeFeatureNeighborsFilter (1 uncovered)

- [ ] L216 (`-24500`): DataArrays with unequal tuple counts

### ComputeFeaturePhasesBinaryFilter (1 uncovered)

- [ ] L122 (`-53800`): DataArrays with unequal tuple counts

### ComputeFeaturePhasesFilter (2 uncovered)

- [ ] L93 (`-4630`): Missing feature ids array
- [ ] L98 (`-4631`): Missing cell features Attribute Matrix

### ComputeFeatureReferenceCAxisMisorientationsFilter (1 uncovered)

- [ ] L114 (`-9800`): DataArrays with unequal tuple counts

### ComputeFeatureReferenceMisorientationsFilter (1 uncovered)

- [ ] L177 (`-94520`): Missing cell feature Attribute Matrix

### ComputeFeatureSizesFilter (2 uncovered)

- [ ] L108: Could not find target geometry
- [ ] L113: Could not find Feature IDs array

### ComputeGBCDFilter (7 uncovered)

- [ ] L125 (`-74350`): Missing euler angles array
- [ ] L129 (`-74351`): Missing phases array
- [ ] L134 (`-74352`): Missing crystal structures array
- [ ] L140 (`-74353`): Missing triangle geometry
- [ ] L149 (`-74354`): Missing face labels array
- [ ] L153 (`-74355`): Missing face normals array
- [ ] L157 (`-74356`): Missing face areas array

### ComputeGBCDPoleFigureFilter (3 uncovered)

- [ ] L110 (`-34640`): Missing crystal structures array
- [ ] L116 (`-34641`): Missing GBCD array
- [ ] L122 (`-34642`): Phase index larger than number of Ensembles

### ComputeIPFColorsFilter (5 uncovered)

- [ ] L123: Crystal structures array with != 1 component
- [ ] L132: Euler angles array with != 3 components
- [ ] L140: Phases array with != 1 component
- [ ] L153: Missing mask array
- [ ] L167 (`-651`): DataArrays with unequal tuple counts

### ComputeMisorientationsFilter (1 uncovered)

- [ ] L141 (`-651`): DataArrays with unequal tuple counts

### ComputeNeighborhoodsFilter (1 uncovered)

- [ ] L115 (`-5730`): DataArrays with unequal tuple counts

### ComputeNumFeaturesFilter (1 uncovered)

- [ ] L95 (`-47630`): Missing ensemble Attribute Matrix

### ComputeQuaternionConjugateFilter (1 uncovered)

- [ ] L99: Quaternion array with != 4 components

### ComputeSchmidsFilter (1 uncovered)

- [ ] L172 (`-13500`): Slip plane and slip direction must be normal

### ComputeShapesFilter (2 uncovered)

- [ ] L118 (`-12801`): Missing cell feature Attribute Matrix
- [ ] L125 (`-12802`): Centroids array wrong type

### ComputeSurfaceFeaturesFilter (1 uncovered)

- [ ] L100 (`-1000`): Image geometry not 3D or 2D

### ComputeVertexToTriangleDistancesFilter (2 uncovered)

- [ ] L108 (`-4530`): DataPath not a valid VertexGeometry
- [ ] L114 (`-4531`): DataPath not a valid TriangleGeometry

### ComputeVolumeFractionsFilter (1 uncovered)

- [ ] L96 (`-47630`): Missing feature Attribute Matrix

### ConvertColorToGrayScaleFilter (2 uncovered)

- [ ] L113 (`-10701`): Invalid color channel selection (not 0, 1, or 2)
- [ ] L141 (`-10700`): Input data array does not exist

### ConvertDataFilter (2 uncovered)

- [ ] L110 (`-15201`): Missing input data array
- [ ] L166 (`-1`): FromSIMPL JSON conversion error

### ConvertOrientationsFilter (1 uncovered)

- [ ] L140: Invalid conversion parameters

### ConvertOrientationsToVertexGeometryFilter (4 uncovered)

- [ ] L124 (`-1001`): Input representation type not 0-6
- [ ] L132 (`-1002`): Input component shape with multiple dimensions
- [ ] L143 (`-1003`): Array validation failure
- [ ] L172 (`-1004`): Array tuple count mismatch

### ConvertQuaternionFilter (1 uncovered)

- [ ] L105: Quaternion array with != 4 components

### CopyFeatureArrayToElementArrayFilter (1 uncovered)

- [ ] L145 (`-3020`): DataArrays with unequal tuple counts

### CreateColorMapFilter (2 uncovered)

- [ ] L133: Missing mask array
- [ ] L147 (`-651`): DataArrays with unequal tuple counts

### CreateGeometryFilter (3 uncovered preflight + 6 other)

- [ ] L239 (`-9840`): Missing vertex list
- [ ] L286 (`-9841`): Missing quadrilateral list
- [ ] L291 (`-9842`): Missing quadrilateral list (second check)

### CropImageGeometryFilter (3 uncovered preflight + 6 other)

- [ ] L279 (`-4010`): No dimension selected to crop
- [ ] L620 (`-950`): Crop bounds validation X
- [ ] L627 (`-951`): Crop bounds validation Y
- [ ] L634 (`-952`): Crop bounds validation Z

### CropVertexGeometryFilter (1 uncovered)

- [ ] L180 (`-58556`): Missing vertex data AttributeMatrix

### EBSDSegmentFeaturesFilter (4 uncovered)

- [ ] L131 (`-655`): Misorientation tolerance == 0
- [ ] L157: Missing mask array
- [ ] L162: Mask array wrong type
- [ ] L170 (`-651`): DataArrays with unequal tuple counts

### ErodeDilateBadDataFilter (1 uncovered)

- [ ] L114 (`-16700`): Operation selection not 0 (Dilate) or 1 (Erode)

### ErodeDilateCoordinationNumberFilter (1 uncovered)

- [ ] L94 (`-16800`): Coordination number not between 0 and 6

### ExtractComponentAsArrayFilter (1 uncovered)

- [ ] L106 (`-45630`): Array component count must be > 1

### ExtractInternalSurfacesFromTriangleGeometryFilter (4 uncovered)

- [ ] L120: Missing geometry validation
- [ ] L128: Missing geometry validation
- [ ] L142: Missing geometry validation
- [ ] L169: Missing geometry validation

### ExtractPipelineToFileFilter (1 uncovered)

- [ ] L153 (`-2582`): Error opening output path

### ExtractVertexGeometryFilter (1 uncovered)

- [ ] L139: Missing mask array

### FillBadDataFilter (1 uncovered)

- [ ] L99 (`-16500`): Minimum allowed defect size < 1

### ITKImageWriterFilter (2 uncovered preflight + 4 other)

- [ ] L352 (`-25600`): Image array dimensions must match ImageGeometry
- [ ] L357 (`-25601`): Fill character should be a single value

### ITKImportImageStackFilter (1 uncovered preflight + 3 other)

- [ ] L850 (`-4`): Unsupported pixel component

### ITKMhaFileReaderFilter (1 uncovered preflight + 1 other)

- [ ] L482 (`-5001`): Error applying transformation — unable to instantiate filter

### InitializeImageGeomCellDataFilter (1 uncovered)

- [ ] L258 (`-3550`): No data arrays selected

### IterativeClosestPointFilter (3 uncovered)

- [ ] L99: Missing geometry validation
- [ ] L104: Missing geometry validation
- [ ] L110: Missing geometry validation

### MergeTwinsFilter (5 uncovered)

- [ ] L145 (`-6874600`): Missing contiguous neighbor list (Int32)
- [ ] L158 (`-6874602`): Missing feature ids array (Int32)
- [ ] L167 (`-6874603`): Missing phases array (Int32)
- [ ] L178 (`-6874602`): Missing average quaternions array (Float32)
- [ ] L191 (`-6874602`): Missing crystal structures array (UInt32)

### NeighborOrientationCorrelationFilter (7 uncovered preflight + 3 other)

- [ ] L120: Missing input image geometry
- [ ] L129: Missing confidence index array
- [ ] L139: Confidence index array wrong type (not 1-component Float32)
- [ ] L147: Missing cell phases array
- [ ] L157: Cell phases wrong type (not 1-component Int32)
- [ ] L165: Missing crystal structures array
- [ ] L175: Crystal structures wrong type (not 1-component UInt32)

### PadImageGeometryFilter (2 uncovered preflight + 1 other)

- [ ] L137 (`-4010`): No dimension selected
- [ ] L147 (`-4115`): Null Image geometry pointer

### PartitionGeometryFilter (1 uncovered preflight + 12 other dataCheck)

- [ ] L378 (`-3010`): Attribute matrix tuple count mismatch with geometry

### QuickSurfaceMeshFilter (2 uncovered)

- [ ] L142 (`-76530`): Missing grid geometry
- [ ] L177 (`-76531`): DataArray wrong tuple count for element data copy

### RandomizeFeatureIdsFilter (1 uncovered)

- [ ] L102 (`-82640`): Attribute Matrix tuple count less than max FeatureId

### ReadAngDataFilter (1 uncovered preflight + 1 other)

- [ ] L108: File validation error

### ReadBinaryCTNorthstarFilter (2 uncovered)

- [ ] L420 (`-38701`): Input header file does not exist
- [ ] L427: Error reading input header file

### ReadChannel5DataFilter (3 uncovered)

- [ ] L120 (`-66500`): Matching .crc file does not exist
- [ ] L124 (`-66501`): std::exception checking file existence
- [ ] L133: File validation error

### ReadCtfDataFilter (1 uncovered)

- [ ] L115: File validation error

### ReadDREAM3DFilter (3 uncovered)

- [ ] L82: Import file path not provided
- [ ] L87: Failed to open HDF5 file
- [ ] L151: Unsupported PathImportPolicy

### ReadH5EbsdFilter (7 uncovered)

- [ ] L113 (`-67500`): Could not read input file
- [ ] L327-L347: Multiple JSON parameter conversion errors (6 checks)

### ReadHDF5DatasetFilter (1 uncovered)

- [ ] L318 (`-21000`): Error reading HDF5 file

### ReadRawBinaryFilter (2 uncovered)

- [ ] L110: Number of components must be positive
- [ ] L125: File is empty

### ReadVolumeGraphicsFileFilter (1 uncovered preflight + 5 other)

- [ ] L446: Volume Graphics data file does not exist

### RemoveFlaggedEdgesFilter (3 uncovered preflight + 2 other)

- [ ] L149 (`-5651`): Missing edge data attribute matrix
- [ ] L157 (`-5652`): Missing edge data attribute matrix (second geom)
- [ ] L179 (`-5653`): Missing vertex data attribute matrix

### RemoveFlaggedFeaturesFilter (2 uncovered)

- [ ] L127 (`-9890`): Missing Feature Ids array
- [ ] L132 (`-9891`): Missing Flagged Features array

### RemoveFlaggedTrianglesFilter (2 uncovered preflight + 2 other)

- [ ] L157 (`-5251`): Missing face data attribute matrix
- [ ] L165 (`-5252`): Missing face data attribute matrix (second check)

### RemoveFlaggedVerticesFilter (4 uncovered)

- [ ] L132: Missing geometry validation
- [ ] L139: Missing geometry validation
- [ ] L167 (`-5751`): Missing cell data attribute matrix
- [ ] L250 (`-54070`): Array validation error

### RequireMinNumNeighborsFilter (1 uncovered)

- [ ] L135: Validation error

### RequireMinimumSizeFeaturesFilter (5 uncovered)

- [ ] L328: Validation error
- [ ] L334: FeatureIds not Int32 Array
- [ ] L339: NumCells not Int32 Array
- [ ] L362: NumCells DataPath has no parent
- [ ] L420 (`-5555`): Validation error

### RobustAutomaticThresholdFilter (1 uncovered)

- [ ] L121: Input array cannot be bool type

### RodriguesConvertorFilter (1 uncovered)

- [ ] L99: Rodrigues array must be 3-component Float32

### RotateSampleRefFrameFilter (1 uncovered)

- [ ] L196 (`-5951`): Missing cell data attribute matrix

### ScalarSegmentFeaturesFilter (6 uncovered)

- [ ] L121: Grid Geometry required
- [ ] L136: Input array must be single component
- [ ] L142: Input array not specified
- [ ] L155: Missing mask array
- [ ] L160: Mask array wrong type
- [ ] L168 (`-651`): DataArrays with unequal tuple counts

### SplitDataArrayByComponentFilter (2 uncovered)

- [ ] L99 (`-65400`): Missing input data array
- [ ] L104 (`-65401`): Array must have > 1 component

### SplitDataArrayByTupleFilter (1 uncovered preflight + 4 other)

- [ ] L418: Missing input array

### SurfaceNetsFilter (1 uncovered)

- [ ] L143 (`-76530`): Missing grid geometry

### TriangleDihedralAngleFilter (2 uncovered)

- [ ] L174 (`-9860`): Missing Triangle Geometry
- [ ] L180 (`-9861`): Missing face data Attribute Matrix

### WriteASCIIDataFilter (1 uncovered)

- [ ] L200 (`-11021`): Unable to create output file

### WriteBinaryDataFilter (1 uncovered)

- [ ] L138 (`-23430`): OutputPath must be a directory

### WriteDREAM3DFilter (2 uncovered)

- [ ] L111: Failed to retrieve pipeline
- [ ] L133: Write validation error

### WriteFeatureDataCSVFilter (2 uncovered)

- [ ] L115 (`-64641`): Error creating output file (parent path)
- [ ] L150 (`-64640`): Error opening path

### WriteGBCDGMTFileFilter (3 uncovered)

- [ ] L111 (`-96710`): Missing crystal structures array
- [ ] L117 (`-96711`): Missing GBCD array
- [ ] L123 (`-96712`): Phase index larger than number of Ensembles

### WriteGBCDTriangleDataFilter (1 uncovered)

- [ ] L109 (`-48320`): DataArrays with unequal tuple counts

### WritePoleFigureFilter (1 uncovered)

- [ ] L199 (`-680000`): MaterialNames not a StringArray

### WriteStatsGenOdfAngleFileFilter (1 uncovered)

- [ ] L134 (`-9402`): DataArrays with unequal tuple counts

### WriteVtkStructuredPointsFilter (1 uncovered)

- [ ] L96 (`-2071`): DataArrays with unequal tuple counts

---

## Summary Statistics

| Category | Count |
|----------|------:|
| Algorithm classes at 0% coverage (real code) | 10 |
| Algorithm classes near-zero (< 10%) | 1 |
| Core utility at 0% | 1 |
| Filters with uncovered preflight error branches | 107 |
| Total uncovered preflight `MakeErrorResult()` calls | 213 |
| Total uncovered non-preflight `MakeErrorResult()` calls | 78 |

### Suggested Priority Order

1. **High-value algorithm tests** — ComputeArrayStatistics (1,288 lines at 9.5%),
ReadDeformKeyFileV12 (840 lines), ComputeGBPDMetricBased (739 lines),
ComputeGBCDMetricBased (612 lines)
2. **Filters with many uncovered branches** — BadDataNeighborOrientationCheckFilter (9),
ApplyTransformationToGeometryFilter (8), ComputeGBCDFilter (7),
NeighborOrientationCorrelationFilter (7), ScalarSegmentFeaturesFilter (6),
ComputeDifferencesMapFilter (6), ReadH5EbsdFilter (7), MergeTwinsFilter (5),
ComputeAvgOrientationsFilter (5), ComputeIPFColorsFilter (5),
RequireMinimumSizeFeaturesFilter (5)
3. **Quick wins** — Filters with only 1-2 uncovered branches where a single
additional test case with bad inputs would cover the error path