midas-plotting 0.3.0__py3-none-any.whl

midas_plotting-0.3.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: midas-plotting
+Version: 0.3.0
+Summary: Standard plots for MIDAS reconstructions - near-field, far-field and Laue: IPF maps and legends, grain maps, pole figures, strain and size distributions, and Laue texture diagnostics against their chance levels.
+Author-email: Hemant Sharma <hsharma@anl.gov>
+License: BSD-3-Clause
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: numpy>=1.22
+Requires-Dist: matplotlib>=3.5
+Requires-Dist: midas-stress>=0.1
+Provides-Extra: dev
+Requires-Dist: pytest>=7; extra == "dev"
+Requires-Dist: scipy>=1.9; extra == "dev"
+
+# midas-plotting
+
+Standard plots for MIDAS reconstructions.
+
+```python
+from midas_plotting import read_mic, orientation_map, compare_maps
+
+m = read_mic("Ce5Y_mr.2.mic")
+print(m.summary())
+orientation_map(m, space_group=225, cmin=0.3)
+```
+
+```bash
+midas-plot Ce5Y.0.mic Ce5Y_sum3thr2.0.mic --kind orientation --cmin 0.3 \
+    --titles "baseline|sum3+thr2" -o compare.png
+```
+
+## Why
+
+IPF colouring, `.mic` parsing and map plotting had been re-implemented in
+several one-off analysis scripts, each with its own conventions. Two things that
+kept going wrong and are now handled in one place:
+
+- **Euler→RGB is not an orientation map.** Two orientations a fraction of a
+  degree apart can produce very different Euler triplets near gimbal lock, so a
+  single grain renders as several colours. `ipf_rgb` colours by the crystal
+  direction along a sample axis instead.
+- **A permissive confidence cut fills the whole grid.** The fit returns *an*
+  orientation for every voxel it evaluates, so plotting at C ≥ 0.1 shows
+  plausible microstructure whether or not material is there. `orientation_map`
+  annotates the figure when asked to plot below `TRUST_FLOOR` (0.3).
+
+Symmetry operators come from `midas_stress`; nothing is hand-listed here.
+
+Implemented Laue families: cubic (SG 195–230) and hexagonal (168–194).
+Anything else raises rather than silently falling back to cubic.
+
+## Far-field (`Grains.csv`)
+
+```python
+from midas_plotting import ff, read_grains
+
+g = read_grains("Grains.csv")
+print(len(g), g.space_group)        # symmetry is read from the file's header
+
+ff.summary(g)                        # one-page overview
+ff.grain_map(g, color="ipf")         # IPF-coloured grain centres
+ff.ipf_legend(g.space_group)         # the colour key
+ff.pole_figure(g, hkl=(1, 1, 1))
+ff.strain_map(g, kind="vonmises")
+```
+
+```bash
+midas-plot Grains.csv --kind summary -o overview.png
+midas-plot Grains.csv --kind pole --hkl 1,1,1
+midas-plot Grains.csv --kind strain --strain-kind hydrostatic
+```
+
+FF output is a **grain list**, not a voxel grid, so these are scatter and
+distribution plots. They are namespaced under `ff` rather than exported flat
+because both modalities have a `grain_map` and they mean different things:
+`maps.grain_map` labels a near-field voxel grid, `ff.grain_map` scatters
+far-field grain centres.
+
+Things the module will not let you get wrong:
+
+* **Symmetry comes from the file.** `Grains.csv` states its space group in the
+  preamble; the plots use it. Defaulting to cubic would colour a hexagonal
+  sample with the wrong IPF triangle and produce a plausible, wrong figure.
+* **Columns are read by name.** `Grains.csv` has 47 columns and
+  `midas-fit-grain` 0.5.6 shipped a cyclic rotation of three of them; a
+  positional reader inherits that silently.
+* **Euler angles are cross-checked against `O11..O33`.** They describe the same
+  orientation, so disagreement means the row is being sliced wrong — you get a
+  warning instead of a wrong colour.
+* **Strain is already microstrain.** The `eFab`/`eKen` columns are not
+  dimensionless; they are not rescaled.
+
+Two caveats the plots cannot fix: FF grain positions are good to ~100 µm (not
+the six decimals the file prints), and `GrainRadius` is only correct with
+`midas-process-grains >= 0.6.1`.
+
+## Laue (`solutions.txt`, `spots.txt`)
+
+```python
+from midas_plotting import laue, read_solutions, read_spots
+
+sol = read_solutions("solutions.txt")     # one row per orientation PER FRAME
+print(sol.summary())                      # ... 4,746 distinct orientations ...
+sol = sol.gate(11)                        # the measured null for THAT scan
+
+c = laue.cluster(sol, 1.0, space_group=194)
+print(c)          # <GrainClusters 631 grains at 1.0deg (of 636 clusters,
+                  #  5 spanning >half the map), n_eff 309.5>
+
+reps = c.representatives(sol.orient_mat)  # one orientation per grain
+laue.tilt_histogram(reps)                 # against the random reference
+laue.texture_strength(reps)               # (peak, chance, peak/chance)
+laue.summary(sol)
+```
+
+```bash
+midas-plot solutions.txt --kind tilt --gate 11 --sg 194
+midas-plot validated.npz --kind summary --sg 194 --tol 1.0
+```
+
+Laue output is neither a voxel grid nor a grain list: it is one row per
+*orientation per frame*, so a crystal seen at twenty positions appears twenty
+times. Nothing is a grain until it has been clustered, and every grain count
+here carries the tolerance that produced it.
+
+Four things the module will not let you get wrong:
+
+* **Half of a random population lies more than 60° from any fixed direction.**
+  That is solid angle, not texture. `tilt_histogram` draws
+  `random_tilt_fractions()` beside the data by default, because "70% of grains
+  lie near the surface plane" reads as a strong texture and is very nearly
+  random — and 30% there is a *depletion*.
+* **A raw pole density is not comparable between datasets.** A small grain
+  population peaks higher by chance alone, and its chance level rises to match.
+  `texture_strength` returns the ratio to its own measured null, which is what
+  makes 85 grains and 631 grains commensurable.
+* **An orientation present at every raster position is not a grain.** The beam
+  moves a micron or two between frames. `cluster` flags anything spanning more
+  than half the map; on one dataset a single such object held 59% of all
+  measurements and dragged the effective sample size from 29 to 2.5. The Kish
+  effective n sits next to every grain count for the same reason.
+* **`orientationRowNr` is column 34 and `misOrientationPostRefinement` is 33.**
+  Reading 33 for 34 does not raise — it returns a near-zero float for every
+  row, so distinct-orientation counts collapse to single digits and the scan
+  looks like it found one crystal. Columns are read by name.
+
+Geometry is explicit, never assumed: `SURFACE_NORMAL_34IDE` and the `COS45`
+stage correction are module constants with 34-ID-E defaults, and every function
+takes `normal=`. The out-of-plane stage axis sits at 45°, so quoting its raw
+extent as a map size understates it by 1.41× — a 200 × 100 µm map reads as
+200 × 71.
+
+The acceptance gate has **no default**. It is the largest number of reflections
+a randomly oriented crystal achieves on those frames, it is a property of the
+scan, and `midas-plot` says so when you omit `--gate` rather than picking one.

midas_plotting-0.3.0.dist-info/RECORD

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+midas_plotting/grains.py,sha256=5JWwRMZRYrKwJ7RdXKJakHvEvqZUiB8HaR-hq7Afs38,11323
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+midas_plotting/mic.py,sha256=q8FyV2vo5J82D4-gY8XXTjGdWwaxAKrIuips9CdVniI,2671
+midas_plotting/solutions.py,sha256=ocOxCkV1Fdx5gENlUw7-IcyDtOh0hznTZQFfnz1OPNs,16461
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midas_plotting-0.3.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (83.0.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

midas_plotting-0.3.0.dist-info/entry_points.txt

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+[console_scripts]
+midas-plot = midas_plotting.cli:main

midas_plotting-0.3.0.dist-info/top_level.txt

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+midas_plotting