diff --git a/Tests/Fixtures/README.md b/Tests/Fixtures/README.md new file mode 100644 index 0000000..39c46d2 --- /dev/null +++ b/Tests/Fixtures/README.md @@ -0,0 +1,173 @@ +# Test fixtures + +One row per committed fixture file under `Tests/*/Fixtures/`: size, the script under `tools/` that names it (the generator or its +pin script; a few scripts write a whole directory; a script found only by file-name prefix, tool-folder name or test module is marked so), and a note where the origin is not the kit's own pinned reference. 152 files. + +Licence: every fixture is generated from this kit's own code and the pinned Python reference (see `CLAUDE.md`, Reference) and ships under the kit's GPL-3.0-or-later licence, except the rows marked *third party*. Nothing here is the owner's data: the committed text fixtures carry no owner path or name (checked by search), and real datasets are read from `$MACEM_DATA` and never copied into the repo. + +## Needs an origin line + +5 fixtures that no script under `tools/` names. They may be written by a directory-level script, by hand, or copied from an earlier kit; a Mac session with the pin scripts fills in the origin and removes the file from this list. + +- `CuboParallaxTests/Fixtures/legacy050.json` +- `CuboVirtualTests/Fixtures/median_3x5.npy` +- `CuboVirtualTests/Fixtures/median_3x5_outlier.npy` +- `CuboVirtualTests/Fixtures/median_4x4.npy` +- `CuboVirtualTests/Fixtures/median_4x4_outlier.npy` + +## All fixtures + +| File | Size | Generated by | Note | +|---|---|---|---| +| `CuboBraggTests/Fixtures/bragg.f64` | 506.4 KB | `tools/bragg/pins.py` | | +| `CuboBraggTests/Fixtures/bragg.json` | 24.3 KB | `tools/bragg/pins.py` | | +| `CuboBraggTests/Fixtures/braggmask.json` | 103.5 KB | `tools/braggmask/pins.py` | | +| `CuboCoreTests/Fixtures/calibration.json` | 682.9 KB | `tools/calibration/pins.py` | | +| `CuboCoreTests/Fixtures/cubeview.json` | 195.2 KB | `tools/cubeview/pins.py` | | +| `CuboCoreTests/Fixtures/frametransform.json` | 6.5 KB | `tools/rereference/pins.py` | | +| `CuboCoreTests/Fixtures/hot-pixels.json` | 29.7 KB | `tools/hot-pixels/pins.py` | | +| `CuboCoreTests/Fixtures/origin-trimmed.json` | 105.7 KB | `tools/origin/trimmed_pins.py` | | +| `CuboEmbeddingTests/Fixtures/appEmbedA.app.f64` | 128 B | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/appEmbedA.in.f64` | 960 B | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/appEmbedB.app.f64` | 512 B | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/appEmbedB.in.f64` | 240 B | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/appEmbedC.app.f64` | 2.0 KB | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/appEmbedC.in.f64` | 2.0 KB | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/appKm3.app.f64` | 792 B | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/appKm3.in.f64` | 2.1 KB | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/appKm4.app.f64` | 816 B | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/appKm4.in.f64` | 2.1 KB | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/appKm5.app.f64` | 800 B | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/appKm5.in.f64` | 3.8 KB | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/embedding.json` | 2.8 KB | `tools/embedding/pins.py` | | +| `CuboEmbeddingTests/Fixtures/kmBlobs.in.f64` | 2.2 KB | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/kmBlobs.sk.f64` | 808 B | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/kmCapped.in.f64` | 2.2 KB | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/kmCapped.sk.f64` | 832 B | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/kmEmpty.in.f64` | 2.2 KB | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/kmEmpty.sk.f64` | 808 B | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/kmTol.in.f64` | 2.2 KB | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/kmTol.sk.f64` | 832 B | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/pcaA.app.f64` | 2.2 KB | `tools/embedding/pins.py` | | +| `CuboEmbeddingTests/Fixtures/pcaA.in.f64` | 3.8 KB | `tools/embedding/pins.py` | | +| `CuboEmbeddingTests/Fixtures/pcaA.sk.f64` | 2.3 KB | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/pcaB.in.f64` | 480 B | `tools/embedding/pins.py` (name prefix) | | +| `CuboEmbeddingTests/Fixtures/pcaB.sk.f64` | 840 B | `tools/embedding/pins.py` (name prefix) | | +| `CuboParallaxTests/Fixtures/aberrations.json` | 17.4 KB | `tools/parallax/aberration_pins.py`, `tools/parallax/app_pins.py` | | +| `CuboParallaxTests/Fixtures/alignment.json` | 161.9 KB | `tools/parallax/pins.py` | | +| `CuboParallaxTests/Fixtures/appvariants.json` | 160.0 KB | `tools/parallax/app_pins.py` | | +| `CuboParallaxTests/Fixtures/depth.json` | 66.2 KB | `tools/parallax/depth_pins.py` | | +| `CuboParallaxTests/Fixtures/legacy050.json` | 45.7 KB | none found | | +| `CuboParallaxTests/Fixtures/preprocess.json` | 110.5 KB | `tools/parallax/preprocess_pins.py`, `tools/ptycho/preprocess_pins.py` | | +| `CuboParallaxTests/Fixtures/reconstruct.json` | 216.7 KB | `tools/parallax/reconstruct_pins.py` | | +| `CuboParallaxTests/Fixtures/subpixel.json` | 100.8 KB | `tools/parallax/subpixel_pins.py` | | +| `CuboPhaseTests/Fixtures/dpcviews.json` | 1.9 KB | `tools/dpcviews/pins.py` | | +| `CuboPhaseTests/Fixtures/idpc.json` | 16.0 KB | `tools/idpc/pins.py` | | +| `CuboPtychoTests/Fixtures/engines.json` | 2.1 MB | `tools/ptycho/engines_pins.py` | | +| `CuboPtychoTests/Fixtures/odd.json` | 877.5 KB | `tools/ptycho/odd_pins.py` | | +| `CuboPtychoTests/Fixtures/options.json` | 273.6 KB | `tools/ptycho/options_pins.py` | | +| `CuboPtychoTests/Fixtures/positions.json` | 564.3 KB | `tools/ptycho/position_pins.py` | | +| `CuboPtychoTests/Fixtures/preprocess.json` | 162.0 KB | `tools/parallax/preprocess_pins.py`, `tools/ptycho/preprocess_pins.py` | | +| `CuboPtychoTests/Fixtures/ptycho.json` | 884.5 KB | `tools/ptycho/options_pins.py`, `tools/ptycho/pins.py` | | +| `CuboStrainTests/Fixtures/appBases.f64` | 192 B | `tools/strain/pins.py` | | +| `CuboStrainTests/Fixtures/appBasis.f64` | 32 B | `tools/strain/pins.py` | | +| `CuboStrainTests/Fixtures/appFits.f64` | 224 B | `tools/strain/pins.py` | | +| `CuboStrainTests/Fixtures/appReference.f64` | 32 B | `tools/strain/pins.py` | | +| `CuboStrainTests/Fixtures/consensus.f64` | 480 B | `tools/strain/pins.py` | | +| `CuboStrainTests/Fixtures/fits.f64` | 224 B | `tools/slice-3/pins.py`, `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (name prefix) | | +| `CuboStrainTests/Fixtures/indexInputs.f64` | 144 B | `tools/strain/pins.py` | | +| `CuboStrainTests/Fixtures/indexOutputs.f64` | 48 B | `tools/strain/pins.py` | | +| `CuboStrainTests/Fixtures/input0.f64` | 360 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/input1.f64` | 360 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/input2.f64` | 360 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/input3.f64` | 480 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_d1_counts.f64` | 448 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_d1_hist.f64` | 18.0 KB | `tools/strain/mapping_pins.py` | | +| `CuboStrainTests/Fixtures/map_d1_peaks.f64` | 28.2 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_d1_truth.f64` | 1.8 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_d2_counts.f64` | 448 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_d2_hist_bool.f64` | 18.0 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_d2_hist_default.f64` | 18.0 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_d2_hist_num.f64` | 18.0 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_d2_hist_s15.f64` | 40.5 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_d2_peaks.f64` | 23.0 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_d2_scanmask.f64` | 448 B | `tools/strain/mapping_pins.py` | | +| `CuboStrainTests/Fixtures/map_d2_truth.f64` | 1.8 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_d2_weights.f64` | 448 B | `tools/strain/mapping_pins.py` | | +| `CuboStrainTests/Fixtures/map_d3_counts.f64` | 512 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_d3_peaks.f64` | 57.4 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r1_basis.f64` | 48 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r1_directions.f64` | 320 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r1_fits.f64` | 3.5 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r1_mask.f64` | 448 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r1_maxima.f64` | 240 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r1_reference.f64` | 32 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r1_strain.f64` | 2.2 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r2_basis.f64` | 48 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r2_directions.f64` | 384 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r2_fits.f64` | 3.5 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r2_mask.f64` | 448 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r2_maxima.f64` | 288 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r2_reference.f64` | 32 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r2_roi.f64` | 448 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r2_strain.f64` | 2.2 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r3_basis.f64` | 48 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r3_directions.f64` | 448 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r3_fits.f64` | 3.5 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r3_mask.f64` | 448 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r3_maxima.f64` | 336 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r3_reference.f64` | 32 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r3_scanmask.f64` | 448 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r3_strain.f64` | 2.2 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r4_basis.f64` | 48 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r4_directions.f64` | 384 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r4_fits.f64` | 3.5 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r4_mask.f64` | 448 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r4_maxima.f64` | 288 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r4_reference.f64` | 32 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r4_strain.f64` | 2.2 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r5_basis.f64` | 48 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r5_directions.f64` | 320 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r5_fits.f64` | 3.5 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r5_mask.f64` | 448 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r5_maxima.f64` | 240 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r5_reference.f64` | 32 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r5_strain.f64` | 2.2 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r6_basis.f64` | 48 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r6_directions.f64` | 256 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r6_fits.f64` | 4.0 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r6_mask.f64` | 512 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r6_maxima.f64` | 192 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r6_reference.f64` | 32 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_r6_strain.f64` | 2.5 KB | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (module only) | | +| `CuboStrainTests/Fixtures/map_ties_ar.f64` | 1.5 KB | `tools/strain/mapping_pins.py` | | +| `CuboStrainTests/Fixtures/map_ties_maxima.f64` | 168 B | `tools/strain/mapping_pins.py` | | +| `CuboStrainTests/Fixtures/maxima.f64` | 192 B | `tools/bragg/pins.py`, `tools/parallax/reconstruct_pins.py`, `tools/strain/mapping_pins.py` +1 | | +| `CuboStrainTests/Fixtures/reference.f64` | 32 B | `tools/bragg/pins.py`, `tools/braggmask/pins.py`, `tools/calibration/pins.py` +18 | | +| `CuboStrainTests/Fixtures/selectedBasis.f64` | 32 B | `tools/strain/pins.py` | | +| `CuboStrainTests/Fixtures/strain.json` | 1.1 KB | `tools/strain/pins.py` | | +| `CuboStrainTests/Fixtures/strain0.f64` | 128 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (name prefix) | | +| `CuboStrainTests/Fixtures/strain1.f64` | 128 B | `tools/strain/mapping_pins.py`, `tools/strain/pins.py` (name prefix) | | +| `CuboStrainTests/Fixtures/strain_mapping.json` | 5.9 KB | `tools/strain/mapping_pins.py` | | +| `CuboVirtualTests/Fixtures/boundary.npy` | 4.1 KB | `tools/idpc/pins.py`, `tools/slice-1/pins.py`, `tools/strain/pins.py` | | +| `CuboVirtualTests/Fixtures/counts16.npy` | 6.9 KB | `tools/slice-1/pins.py`, `tools/slice-3/pins.py`, `tools/slice-4/pins.py` | | +| `CuboVirtualTests/Fixtures/counts32.npy` | 3.9 KB | `tools/slice-1/pins.py` | | +| `CuboVirtualTests/Fixtures/digits.npy` | 968 B | `tools/parallax/reconstruct_pins.py`, `tools/ptycho/engines_pins.py`, `tools/slice-1/pins.py` | | +| `CuboVirtualTests/Fixtures/friedel_gauss.npy` | 18.9 KB | `tools/slice-4/pins.py` | | +| `CuboVirtualTests/Fixtures/friedel_masked.npy` | 25.6 KB | `tools/slice-4/pins.py` | | +| `CuboVirtualTests/Fixtures/friedel_plain.npy` | 25.6 KB | `tools/slice-4/pins.py` | | +| `CuboVirtualTests/Fixtures/gaussian.npy` | 30.1 KB | `tools/bragg/pins.py`, `tools/parallax/app_pins.py`, `tools/parallax/subpixel_pins.py` +8 | | +| `CuboVirtualTests/Fixtures/median_3x5.npy` | 2.6 KB | none found | | +| `CuboVirtualTests/Fixtures/median_3x5_outlier.npy` | 2.6 KB | none found | | +| `CuboVirtualTests/Fixtures/median_4x4.npy` | 2.8 KB | none found | | +| `CuboVirtualTests/Fixtures/median_4x4_outlier.npy` | 2.8 KB | none found | | +| `CuboVirtualTests/Fixtures/negative.npy` | 272 B | `tools/dpcviews/pins.py`, `tools/embedding/pins.py`, `tools/ptycho/engines_pins.py` +3 | | +| `CuboVirtualTests/Fixtures/planted_f32.npy` | 70.4 KB | `tools/slice-3/pins.py`, `tools/slice-4/pins.py` | | +| `CuboVirtualTests/Fixtures/planted_u16.npy` | 35.3 KB | `tools/slice-3/pins.py`, `tools/slice-4/pins.py` | | +| `CuboVirtualTests/Fixtures/shift.npy` | 5.8 KB | `tools/slice-2/pins.py` | | +| `CuboVirtualTests/Fixtures/slice-1-pins.json` | 204.9 KB | `tools/slice-1/pins.py`, `tools/slice-2/pins.py` | | +| `CuboVirtualTests/Fixtures/slice-2-pins.json` | 596.1 KB | `tools/slice-2/pins.py` | | +| `CuboVirtualTests/Fixtures/slice-3-pins.json` | 324.2 KB | `tools/slice-3/pins.py` | | +| `CuboVirtualTests/Fixtures/slice-4-pins.json` | 1.7 MB | `tools/slice-4/pins.py` | | +| `CuboVirtualTests/Fixtures/thirds.npy` | 640 B | `tools/slice-1/pins.py` | | +| `CuboVirtualTests/Fixtures/vacuum_planted.npy` | 24.1 KB | `tools/slice-4/pins.py` | |