WIP Add layer map to report

ashlar/report.py

@@ -43,6 +43,13 @@ def generate_report(path, aligners):
     pdf.add_figure(fig, "Cycle 1: Tile pair alignment quality")
     plt.close(fig)
 
+    for i, aligner in enumerate(aligners, 2):
+        pdf.add_page()
+        fig = plot_layer_map(aligner, aligner.reader.thumbnail)
+        fig.set_size_inches(7.5, 9)
+        pdf.add_figure(fig, f"Cycle {i}: Cycle alignment map")
+        plt.close(fig)
+
     pdf.output(path)
 
 
@@ -133,14 +140,7 @@ def plot_edge_map(
         **nx_kwargs,
     )
     nx.draw_networkx_labels(g, pos, ax=ax, font_size=font_size, **nx_kwargs)
-    rh, rw = aligner.metadata.size
-    for x, y in pos:
-        x -= rw / 2
-        y -= rh / 2
-        rect = mpatches.Rectangle(
-            (x, y), rw, rh, color='silver', alpha=0.25, fill=False, lw=0.25, zorder=0.5
-        )
-        ax.add_patch(rect)
+    draw_borders(ax, aligner, pos)
     cbar = fig.colorbar(
         mcm.ScalarMappable(mcolors.Normalize(emin, emax), edge_cmap),
         extend="max",
@@ -247,7 +247,7 @@ def plot_layer_map(
     im_kwargs=None,
     nx_kwargs=None,
 ):
-    """Plot tile centers colored by shift distance"""
+    """Plot tile shift distance and direction"""
 
     if pos == "metadata":
         centers = aligner.metadata.centers - aligner.metadata.origin
@@ -261,31 +261,69 @@ def plot_layer_map(
     fig, ax = plt.subplots()
     draw_mosaic_image(ax, aligner, img, cmap=cmap, **im_kwargs)
 
-    # FIXME colors are wrong -- how do lists passed to draw_networkx_nodes need
-    # to be organized/sorted?
     shifts = np.linalg.norm(aligner.shifts, axis=1)
     skeep = shifts[~aligner.discard]
     smin, smax = (skeep.min(), skeep.max()) if len(skeep) > 0 else (0, 0)
     # Map discards to the "over" color in the cmap.
     shifts[aligner.discard] = smax + 1
+    # Reorder to match the graph's internal node ordering.
+    node_values = shifts[np.array(aligner.neighbors_graph)]
 
     diameter = nx.diameter(aligner.neighbors_graph)
     drange = [10, 60]
     interp = functools.partial(np.interp, diameter, drange)
     node_size = node_size or interp([100, 8])
     font_size = font_size or interp([6, 2])
-    font_color = np.where(aligner.discard, "w", "k")
-    node_cmap = mcm.Greens.with_extremes(over=(0.15, 0.15, 0.15))
+    node_cmap = mcm.Greens.with_extremes(over="#252525")
     g = aligner.neighbors_graph
     pos = np.fliplr(centers)
+    qlen = np.min(aligner.metadata.size) * 0.45
+    q_angles = np.rad2deg(np.arctan2(*aligner.shifts.T)) # FIXME: invert Y?
+    reference_offset = (
+        aligner.cycle_offset
+        + aligner.metadata.origin
+        - aligner.reference_aligner.metadata.origin
+    )
+    reference_corners = (
+        aligner.reference_aligner.metadata.centers
+        - aligner.reference_aligner.metadata.origin
+        + aligner.reference_aligner.metadata.size / 2
+    )
+    reference_size = np.max(reference_corners, axis=0)
+
+    ax.add_patch(
+        mpatches.Rectangle(
+            -reference_offset[::-1],
+            *np.max(centers + aligner.metadata.size / 2, axis=0)[::-1],
+            color=mcm.Blues(0.75),
+            lw=2,
+            linestyle="--",
+            fill=False,
+        )
+    )
+    ax.quiver(
+        pos[:, 0],
+        pos[:, 1],
+        [qlen] * len(pos),
+        [0] * len(pos),
+        shifts,
+        cmap=node_cmap,
+        clim=(smin, smax),
+        angles=q_angles,
+        scale_units="x",
+        scale=1,
+        headwidth=1,
+        headlength=1,
+        headaxislength=1,
+    )
     nx.draw_networkx_nodes(
         g,
         pos,
         ax=ax,
         cmap=node_cmap,
         vmin=smin,
         vmax=smax,
-        node_color=shifts,
+        node_color=node_values,
         node_size=node_size,
         edgecolors=None,
         **nx_kwargs,
@@ -297,17 +335,9 @@ def plot_layer_map(
         font_size=font_size,
         **nx_kwargs,
     )
-    nodes = np.arange(len(g))
-    draw_labels(g.subgraph(nodes[aligner.discard]), font_color="gray")
-    draw_labels(g.subgraph(nodes[~aligner.discard]), font_color="k")
-    rh, rw = aligner.metadata.size
-    for x, y in pos:
-        x -= rw / 2
-        y -= rh / 2
-        rect = mpatches.Rectangle(
-            (x, y), rw, rh, color='silver', alpha=0.25, fill=False, lw=0.25, zorder=0.5
-        )
-        ax.add_patch(rect)
+    draw_labels(g.subgraph(np.nonzero(aligner.discard)[0]), font_color="gray")
+    draw_labels(g.subgraph(np.nonzero(~aligner.discard)[0]), font_color="k")
+    draw_borders(ax, aligner, pos)
     cbar = fig.colorbar(
         mcm.ScalarMappable(mcolors.Normalize(smin, smax), node_cmap),
         extend="max",
@@ -319,26 +349,8 @@ def plot_layer_map(
     ax.set_frame_on(False)
     ax.margins(0)
     fig.tight_layout()
-
     return fig
 
-    if artist == 'quiver':
-        ax.quiver(
-            *centers.T[::-1], *shifts.T[::-1], aligner.discard,
-            units='dots', width=2, scale=1, scale_units='xy', angles='xy',
-            cmap='Greys'
-        )
-    if artist == 'patches':
-        for xy, dxy, is_discarded in zip(
-            np.fliplr(centers), np.fliplr(shifts), aligner.discard
-        ):
-            arrow = mpatches.FancyArrowPatch(
-                xy, np.array(xy) + np.array(dxy), 
-                arrowstyle='->', color='0' if is_discarded else '1',
-                mutation_scale=8,
-                )
-            ax.add_patch(arrow)
-
 
 def draw_mosaic_image(ax, aligner, img, **kwargs):
     if img is None:
@@ -350,3 +362,18 @@ def draw_mosaic_image(ax, aligner, img, **kwargs):
     if "vmax" not in kwargs:
         kwargs["vmax"] = np.percentile(img, 99)
     ax.imshow(img, extent=(-0.5, w-0.5, h-0.5, -0.5), **kwargs)
+
+
+def draw_borders(ax, aligner, pos):
+    rh, rw = aligner.metadata.size
+    for x, y in pos - (rw / 2, rh / 2):
+        rect = mpatches.Rectangle(
+            (x, y),
+            rw,
+            rh,
+            color=(0.2, 0.2, 0.2),
+            fill=False,
+            lw=0.25,
+            zorder=0.5,
+        )
+        ax.add_patch(rect)

ashlar/scripts/ashlar.py

@@ -296,14 +296,14 @@ def process_single(
         edge_aligner.reader.reader.thumbnail = edge_aligner.reader.thumbnail
     edge_aligner.reader = edge_aligner.reader.reader
 
-    if not quiet:
-        print()
-        print(f"Merging tiles and writing to {output_path_format}")
-    writer_class = reg.PyramidWriter if pyramid else reg.TiffListWriter
-    writer = writer_class(
-        mosaics, output_path_format, verbose=not quiet, **writer_args
-    )
-    writer.run()
+    # if not quiet:
+    #     print()
+    #     print(f"Merging tiles and writing to {output_path_format}")
+    # writer_class = reg.PyramidWriter if pyramid else reg.TiffListWriter
+    # writer = writer_class(
+    #     mosaics, output_path_format, verbose=not quiet, **writer_args
+    # )
+    # writer.run()
 
     if report_path:
         generate_report(report_path, [m.aligner for m in mosaics])