midas-plotting 0.4.1__tar.gz → 0.5.0__tar.gz

{midas_plotting-0.4.1 → midas_plotting-0.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: midas-plotting
-Version: 0.4.1
+Version: 0.5.0
 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

{midas_plotting-0.4.1 → midas_plotting-0.5.0}/midas_plotting/__init__.py

@@ -48,7 +48,7 @@ from .solutions import (
 )
 from .mic import MicMap, read_mic
 
-__version__ = "0.4.1"
+__version__ = "0.5.0"
 __all__ = [
     "MicMap", "read_mic", "GrainList", "read_grains", "ff", "laue",
     "LaueSolutions", "LaueSpots", "read_solutions", "read_spots",

{midas_plotting-0.4.1 → midas_plotting-0.5.0}/midas_plotting/ff.py

@@ -26,7 +26,8 @@ from typing import Optional, Sequence
 import numpy as np
 
 from .grains import GrainList, read_grains
-from .ipf import direction_rgb, ipf_rgb_from_matrix, laue_class, sym_matrices, CUBIC
+from .ipf import (direction_rgb, ipf_rgb_from_matrix, laue_class, sym_matrices,
+                  sector_deg, triangle_corners, CUBIC)
 
 __all__ = [
     "ipf_legend", "grain_map", "grain_map_3d", "grain_size_distribution",
@@ -96,11 +97,13 @@ def ipf_legend(space_group: int = 225, ax=None, *, n: int = 400,
 
     fam = laue_class(space_group)
     # Sample the stereographic plane, back-project to directions, keep the ones
-    # already inside the standard triangle.
-    if fam == CUBIC:
-        corners = np.array([[0, 0, 1.0], [1, 0, 1.0], [1, 1, 1.0]])
-    else:
-        corners = np.array([[0, 0, 1.0], [1, 0, 0.0], [np.sqrt(3) / 2, 0.5, 0.0]])
+    # already inside the standard triangle. Corners and the azimuthal sector
+    # come from midas_plotting.ipf, the SAME source the colour ramps fold by,
+    # so the key cannot describe a different triangle from the one drawn. The
+    # `else` branch here used to hard-code the 30 deg hexagonal triangle, which
+    # would have drawn a hexagonal key over a 4/mmm map once the tetragonal and
+    # orthorhombic triangles were added.
+    corners, labels = triangle_corners(space_group)
     # Normalise BEFORE projecting: the stereographic map is defined on unit
     # vectors. Projecting the raw index triple puts [111] at (0.5, 0.5)
     # instead of (0.366, 0.366), so the corner marker and its label sit
@@ -122,7 +125,8 @@ def ipf_legend(space_group: int = 225, ax=None, *, n: int = 400,
                  (d[:, 1] <= d[:, 0] + 1e-9) & (d[:, 0] <= d[:, 2] + 1e-9)
     else:
         az = np.degrees(np.arctan2(d[:, 1], d[:, 0]))
-        inside = (d[:, 2] >= -1e-9) & (az >= -1e-9) & (az <= 30.0 + 1e-9)
+        inside = (d[:, 2] >= -1e-9) & (az >= -1e-9) & \
+                 (az <= sector_deg(space_group) + 1e-9)
 
     rgb = np.ones((d.shape[0], 3))
     if inside.any():
@@ -132,8 +136,6 @@ def ipf_legend(space_group: int = 225, ax=None, *, n: int = 400,
 
     ax.imshow(img, origin="lower", alpha=alpha,
               extent=(x0, x1, y0, y1))
-    labels = (["[001]", "[101]", "[111]"] if fam == CUBIC
-              else ["[0001]", r"[10$\bar{1}$0]", r"[2$\bar{1}\bar{1}$0]"])
     for (px, py), lab in zip(zip(cx, cy), labels):
         ax.plot(px, py, "k.", ms=4)
         ax.annotate(lab, (px, py), textcoords="offset points",

{midas_plotting-0.4.1 → midas_plotting-0.5.0}/midas_plotting/ipf.py

@@ -13,21 +13,35 @@ from __future__ import annotations
 
 from typing import Sequence
 
+import math
 import numpy as np
 
-__all__ = ["ipf_rgb", "sym_matrices", "CUBIC", "HEXAGONAL", "TRIGONAL"]
+__all__ = ["ipf_rgb", "ipf_rgb_from_matrix", "direction_rgb", "laue_class",
+           "sym_matrices", "sector_deg", "triangle_corners",
+           "CUBIC", "HEXAGONAL", "TRIGONAL", "TETRAGONAL", "ORTHORHOMBIC"]
 
 CUBIC = "cubic"
+TETRAGONAL = "tetragonal"
+ORTHORHOMBIC = "orthorhombic"
 HEXAGONAL = "hexagonal"
 TRIGONAL = "trigonal"
 
 # Laue class per space-group range, for the ones MIDAS actually reconstructs.
 # Deliberately explicit rather than clever: a wrong guess here silently
 # recolours a map without any other symptom.
+#
+# The ranges are LAUE CLASSES, not crystal systems, and the two do not coincide
+# in the tetragonal case: 89-142 is 4/mmm, whose triangle closes at 45 deg on
+# [110], while 75-88 is 4/m, which has no in-plane mirror and whose triangle
+# spans the full 90 deg to [010]. Colouring a 4/m crystal with the 4/mmm
+# triangle folds by a 2-fold it does not have, so 75-88 is left OUT and refuses
+# rather than guessing. Implement `_rgb_tetragonal_4m` before widening it.
 _SG_LAUE = [
     (195, 230, CUBIC),
     (168, 194, HEXAGONAL),
     (143, 167, TRIGONAL),
+    (89, 142, TETRAGONAL),      # 4/mmm only -- see the note above
+    (16, 74, ORTHORHOMBIC),
 ]
 
 
@@ -43,7 +57,10 @@ def laue_class(space_group: int) -> str:
             return name
     raise NotImplementedError(
         f"IPF colouring for space group {space_group} is not implemented "
-        f"(have: cubic 195-230, hexagonal 168-194, trigonal 143-167). Refusing to guess."
+        f"(have: cubic 195-230, hexagonal 168-194, trigonal 143-167, "
+        f"tetragonal 4/mmm 89-142, orthorhombic 16-74). Refusing to guess. "
+        f"Note 75-88 is Laue class 4/m, whose triangle spans 90 deg, not the "
+        f"45 deg of 4/mmm; it is deliberately not implemented."
     )
 
 
@@ -69,6 +86,38 @@ def _rgb_cubic(d: np.ndarray) -> np.ndarray:
     return rgb
 
 
+
+def _rgb_tetragonal(d: np.ndarray) -> np.ndarray:
+    """Standard [001]-[100]-[110] triangle for Laue class 4/mmm.
+
+    Same construction as :func:`_rgb_hexagonal`: red is the c-axis component,
+    and the in-plane azimuth interpolates green -> blue across the triangle's
+    angular width, here 45 degrees rather than 30. Added for I4/mmm (SG 139),
+    the Ruddlesden-Popper subcell — before this the function raised, which was
+    correct: colouring a tetragonal crystal with the cubic triangle folds by a
+    3-fold the crystal does not have.
+    """
+    dz = np.abs(d[:, 2])
+    planar = np.hypot(d[:, 0], d[:, 1])
+    phi = np.degrees(np.arctan2(np.abs(d[:, 1]), np.abs(d[:, 0])))
+    phi = np.minimum(phi % 90.0, 90.0 - (phi % 90.0))      # fold to [0, 45]
+    t = np.clip(phi / 45.0, 0.0, 1.0)
+    return np.stack([dz, planar * (1.0 - t), planar * t], axis=1)
+
+
+def _rgb_orthorhombic(d: np.ndarray) -> np.ndarray:
+    """Standard [001]-[100]-[010] triangle for Laue class mmm.
+
+    The triangle spans a full 90 degrees of azimuth because mmm has no
+    in-plane rotation relating a to b. Added for Fmmm (SG 69).
+    """
+    dz = np.abs(d[:, 2])
+    planar = np.hypot(d[:, 0], d[:, 1])
+    phi = np.degrees(np.arctan2(np.abs(d[:, 1]), np.abs(d[:, 0])))
+    t = np.clip(phi / 90.0, 0.0, 1.0)
+    return np.stack([dz, planar * (1.0 - t), planar * t], axis=1)
+
+
 def _rgb_hexagonal(d: np.ndarray) -> np.ndarray:
     """Standard [0001]-[10-10]-[2-1-10] triangle.
 
@@ -233,6 +282,14 @@ def direction_rgb(
         rgb = _rgb_cubic(red)
     elif fam == TRIGONAL:
         rgb = _rgb_trigonal(d, sym)
+    elif fam in (TETRAGONAL, ORTHORHOMBIC):
+        dd = d.copy()
+        dd[:, :, 2] = np.abs(dd[:, :, 2])
+        pick = np.argmax(dd[:, :, 2], axis=1)          # closest to [001]
+        red = dd[np.arange(dd.shape[0]), pick]
+        red /= np.linalg.norm(red, axis=1, keepdims=True)
+        rgb = (_rgb_tetragonal(red) if fam == TETRAGONAL
+               else _rgb_orthorhombic(red))
     else:
         dd = d.copy()
         dd[:, :, 2] = np.abs(dd[:, :, 2])
@@ -245,3 +302,45 @@ def direction_rgb(
     mx = rgb.max(axis=1, keepdims=True)
     rgb = np.where(mx > 0, rgb / mx, rgb)
     return np.clip(rgb ** float(gamma), 0.0, 1.0)
+
+def sector_deg(space_group: int) -> float:
+    """Azimuthal width of the standard triangle, in degrees.
+
+    The SAME number the colour ramps fold by, so a legend built from this
+    cannot disagree with the map it explains. Cubic is excluded: its triangle
+    closes on [111], not on an in-plane direction, so an azimuth does not
+    describe it.
+    """
+    fam = laue_class(space_group)
+    if fam == CUBIC:
+        raise ValueError("the cubic triangle is not defined by an azimuth; "
+                         "its third corner is [111]")
+    if fam == TETRAGONAL:
+        return 45.0
+    if fam == ORTHORHOMBIC:
+        return 90.0
+    if fam == HEXAGONAL:
+        return 30.0
+    if fam == TRIGONAL:
+        return _trigonal_sector_deg(sym_matrices(space_group))
+    raise NotImplementedError(f"no triangle implemented for {fam}")
+
+
+def triangle_corners(space_group: int):
+    """``(corners, labels)`` for the standard triangle of this Laue class.
+
+    Cubic closes on [111]; every other implemented class is
+    [001] - [100] - (the in-plane direction at :func:`sector_deg`).
+    """
+    fam = laue_class(space_group)
+    if fam == CUBIC:
+        return (np.array([[0., 0., 1.], [1., 0., 1.], [1., 1., 1.]]),
+                ["[001]", "[101]", "[111]"])
+    phi = math.radians(sector_deg(space_group))
+    corners = np.array([[0., 0., 1.], [1., 0., 0.],
+                        [math.cos(phi), math.sin(phi), 0.]])
+    lab = {TETRAGONAL:   ["[001]", "[100]", "[110]"],
+           ORTHORHOMBIC: ["[001]", "[100]", "[010]"],
+           HEXAGONAL:    ["[0001]", r"[10$\bar{1}$0]", r"[2$\bar{1}\bar{1}$0]"],
+           TRIGONAL:     ["[0001]", r"[10$\bar{1}$0]", r"[01$\bar{1}$0]"]}[fam]
+    return corners, lab

{midas_plotting-0.4.1 → midas_plotting-0.5.0}/midas_plotting.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: midas-plotting
-Version: 0.4.1
+Version: 0.5.0
 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

{midas_plotting-0.4.1 → midas_plotting-0.5.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "midas-plotting"
-version = "0.4.1"
+version = "0.5.0"
 description = "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."
 readme = "README.md"
 license = { text = "BSD-3-Clause" }

{midas_plotting-0.4.1 → midas_plotting-0.5.0}/tests/test_ipf.py

@@ -21,11 +21,53 @@ def test_laue_class_known_families():
 
 
 def test_laue_class_refuses_unimplemented_rather_than_guessing():
-    """A silent fallback to cubic would recolour a map with no other symptom."""
-    with pytest.raises(NotImplementedError, match="not implemented"):
-        laue_class(2)          # triclinic
+    """A silent fallback to cubic would recolour a map with no other symptom.
+
+    SG 139 (tetragonal) and 69 (orthorhombic) were on this list until their
+    triangles were implemented; triclinic and monoclinic still are not, and the
+    contract is that they REFUSE rather than guess.
+
+    SG 75-88 is the subtle one. It is tetragonal by CRYSTAL SYSTEM but its Laue
+    class is 4/m, not 4/mmm: no in-plane mirror, so its triangle spans 90 deg to
+    [010] rather than 45 deg to [110]. Colouring it with the 4/mmm ramp folds by
+    a 2-fold the crystal does not have and yields a plausible, wrong map. It is
+    deliberately excluded until `_rgb_tetragonal_4m` exists.
+    """
+    for sg in (1, 2, 5, 15):                      # triclinic + monoclinic
+        with pytest.raises(NotImplementedError, match="not implemented"):
+            laue_class(sg)
+    for sg in (75, 81, 88):                       # Laue class 4/m, NOT 4/mmm
+        with pytest.raises(NotImplementedError, match="not implemented"):
+            laue_class(sg)
+
+
+def test_tetragonal_range_is_the_laue_class_not_the_crystal_system():
+    """4/mmm starts at 89. The boundary is the whole point of the split."""
+    from midas_plotting.ipf import laue_class, sector_deg, TETRAGONAL
     with pytest.raises(NotImplementedError):
-        laue_class(139)        # tetragonal
+        laue_class(88)
+    assert laue_class(89) == TETRAGONAL
+    assert sector_deg(89) == 45.0 and sector_deg(142) == 45.0
+
+
+def test_tetragonal_and_orthorhombic_triangles_are_distinct():
+    """4/mmm and mmm must not be the same colouring, and neither may be cubic.
+
+    The discriminator is [010]: under 4/mmm a 4-fold makes it equivalent to
+    [100] (both GREEN), while mmm has no in-plane rotation so [010] is the
+    third vertex (BLUE). A tetragonal map coloured with the mmm triangle -- or
+    with the cubic one, which folds by a 3-fold the crystal does not have --
+    would look plausible and be wrong.
+    """
+    import numpy as np
+    from midas_plotting.ipf import direction_rgb
+    dirs = np.array([[0., 0., 1.], [1., 0., 0.], [0., 1., 0.]])
+    tet = direction_rgb(dirs, space_group=139)
+    ort = direction_rgb(dirs, space_group=69)
+    assert tet[0, 0] > 0.9 and ort[0, 0] > 0.9        # [001] is red in both
+    assert np.allclose(tet[1], tet[2], atol=1e-6), "4/mmm: [100] and [010] must match"
+    assert not np.allclose(ort[1], ort[2], atol=0.5), "mmm: [100] and [010] must differ"
+    assert ort[2, 2] > 0.9, "mmm: [010] is the blue vertex"
 
 
 def test_sym_matrices_are_proper_rotations():