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Replace the two Fusion alignment actions with a three-step wizard

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Alignment was two disconnected menu actions. `Angle Alignment` ran the
registration with ref_angle_idx hard-coded to 0, no exposed parameters and
no way to retry; `Manual Alignment...` was a separate dialog that
deliberately refused to inherit the automatic result, so a bad fit meant
starting over by hand. Neither told you whether the alignment was any
good, and neither produced anything durable beyond an in-memory result.

Fusion -> Alignment Wizard... now covers all of it in three steps:

  1. Correlate. Reference angle, DC threshold, source, rotation seed and
     sign, search window, coarse step and fine grid are all on the page,
     and Run/Re-run is repeatable. Angles start pre-rotated from the
     stage angles in the file, so the page is informative before any
     correlation runs. The verdict is a picture: every angle's DC mask
     reprojected onto the shared canvas and summed, coloured by how many
     angles cover each pixel, so a good alignment reads as one saturated
     plateau and a bad one as a fringe of low-count halos. A per-angle
     fit table flags angles that did not register or that disagree with
     their stage angle by more than a degree.
  2. Crop. An axis-aligned rectangle on that canvas, with numeric
     canvas-pixel boxes synced both ways and a live size estimate.
     "Fit to full overlap" uses a largest-rectangle sweep rather than a
     bounding box: the overlap region of several rotated scans is roughly
     a disc, whose bounding box has corners no angle covers.
  3. Save. Writes the aligned, cropped stack to a new .sras.

Because the wizard replaces both actions it absorbs the old dialog's
by-eye nudge editor — without it, a scan the search cannot fit would
have no fallback at all. ManualAlignmentDialog is therefore deleted
rather than left orphaned, and its tests move to the wizard.

Two bugs found while driving it end to end and fixed here: QSpinBox
setRange clamps and emits valueChanged, which committed a 1x1 crop
before the default preset could run; and the mm round trip returns an
exact pixel boundary as 11.000000000000002, so a bare ceil() added a
spurious column on every rectangle edit.

Verified: 103 pass, the 6 test_stored_cache failures are pre-existing on
main, and tools/check_equivalence.py is byte-identical to main.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
This commit is contained in:
Thomas Ales
2026-08-07 23:00:59 -05:00
parent 6d0e30b9ce
commit f40c965b74
15 changed files with 2037 additions and 964 deletions
Download Patch File Download Diff File Expand all files Collapse all files
sras_viewer/canvases.py
+32 -13
View File
@@ -13,6 +13,27 @@ from PyQt6.QtWidgets import QSizePolicy
from sras_format import CH1_IDX, CH3_IDX, CH4_IDX, CH_NAMES, SrasFile, adc_to_mv
def count_colormap(n_angles: int):
"""(cmap, norm, ticks) for an integer "how many angles cover this pixel"
image, 0..n_angles.
Discrete, not continuous: the judgement the wizard's stack view exists for
is "is this a plateau at N, or a fan of partial overlaps", so a region
covered by one angle too few has to read as its own band rather than a
slightly darker shade. Count 0 is fully transparent so uncovered canvas
cannot be mistaken for a low count.
Shared by both wizard pages that draw this image — they use different canvas
classes, and the same number must not change colour between them.
"""
n = max(1, int(n_angles))
base = mpl.colormaps["viridis"].resampled(n)
colors = [(0.0, 0.0, 0.0, 0.0)] + [base(i) for i in range(n)]
return (ListedColormap(colors),
BoundaryNorm(np.arange(-0.5, n + 1), len(colors)),
np.arange(0, n + 1))
# ---------------------------------------------------------------------------
# ROI (free quadrilateral in data coordinates)
# ---------------------------------------------------------------------------
@@ -145,10 +166,11 @@ class ImageCanvas(FigureCanvasQTAgg):
def show_image(self, img: np.ndarray, extent: list[float], cmap,
vmin: float, vmax: float, xlabel: str, ylabel: str, title: str,
colorbar_label: str = "", cb_ticks=None):
"""*cmap* may be a name or a Colormap instance; *cb_ticks* pins the
colorbar's ticks, which the wizard's integer overlap-count view needs so
each band reads as a whole number of angles rather than a shade."""
colorbar_label: str = "", cb_ticks=None, norm=None):
"""*cmap* may be a name or a Colormap instance. *norm* (which overrides
vmin/vmax) and *cb_ticks* let a caller draw a discrete integer image —
the wizard's overlap-count view — with whole-number colorbar bands
instead of a continuous shade."""
self.figure.clf()
self.ax = self.figure.add_subplot(111)
# Patches and lines are destroyed by figure.clf(); drop stale refs.
@@ -157,10 +179,11 @@ class ImageCanvas(FigureCanvasQTAgg):
self._extent = extent
self._img_shape = img.shape
kw = ({"norm": norm} if norm is not None
else {"vmin": vmin, "vmax": vmax})
im = self.ax.imshow(
img, aspect="auto", origin="upper",
extent=extent, cmap=cmap, vmin=vmin, vmax=vmax,
interpolation="nearest",
extent=extent, cmap=cmap, interpolation="nearest", **kw,
)
cb = self.figure.colorbar(im, ax=self.ax, fraction=0.046, pad=0.04,
ticks=cb_ticks)
@@ -576,16 +599,12 @@ class AlignOverlayCanvas(FigureCanvasQTAgg):
"""
self.figure.clf()
self.ax = self.figure.add_subplot(111)
n = max(1, int(n_angles))
colors = [(0.0, 0.0, 0.0, 0.0)] # count 0: nothing
base = mpl.colormaps["viridis"].resampled(n)
colors += [base(i) for i in range(n)]
cmap, norm, ticks = count_colormap(n_angles)
im = self.ax.imshow(
np.asarray(counts), extent=extent, origin="upper", aspect="auto",
interpolation="nearest", cmap=ListedColormap(colors),
norm=BoundaryNorm(np.arange(-0.5, n + 1), len(colors)))
interpolation="nearest", cmap=cmap, norm=norm)
cb = self.figure.colorbar(im, ax=self.ax, fraction=0.046, pad=0.04,
ticks=np.arange(0, n + 1))
ticks=ticks)
cb.set_label("angles overlapping")
self._finish(title)