try to fix recons

atlas/tasks.py

@@ -336,6 +336,32 @@ def series_reconstruct_task(
     src_y = source_for_patient_axis[1]
     src_z = source_for_patient_axis[2]
 
+    # Build patient-axis basis vectors expressed in source/world space.
+    # This preserves source world-frame orientation (including obliquity/sign)
+    # for derived series instead of hardcoding cardinal axes.
+    patient_x_vec = np.asarray(source_axis_dirs[src_x], dtype=float) * float(sign_for_patient_axis[0])
+    patient_y_vec = np.asarray(source_axis_dirs[src_y], dtype=float) * float(sign_for_patient_axis[1])
+    patient_z_vec = np.asarray(source_axis_dirs[src_z], dtype=float) * float(sign_for_patient_axis[2])
+
+    def _norm_vec(vec):
+        nrm = float(np.linalg.norm(vec))
+        if nrm == 0:
+            return np.asarray(vec, dtype=float)
+        return np.asarray(vec, dtype=float) / nrm
+
+    patient_x_vec = _norm_vec(patient_x_vec)
+    patient_y_vec = _norm_vec(patient_y_vec)
+    patient_z_vec = _norm_vec(patient_z_vec)
+
+    def _orientation_pair(col_vec, row_vec, desired_normal):
+        col = _norm_vec(col_vec)
+        row = _norm_vec(row_vec)
+        desired = _norm_vec(desired_normal)
+        normal = np.cross(col, row)
+        if float(np.dot(normal, desired)) < 0:
+            row = -row
+        return [float(col[0]), float(col[1]), float(col[2]), float(row[0]), float(row[1]), float(row[2])]
+
     spacing_x = source_axis_spacings[src_x]
     spacing_y = source_axis_spacings[src_y]
     spacing_z = source_axis_spacings[src_z]
@@ -350,7 +376,7 @@ def series_reconstruct_task(
         vol_zyx = np.flip(vol_zyx, axis=2)
 
     def source_indices_from_patient_zyx(iz, iy, ix):
-        src_indices = [0, 0, 0]
+        src_indices = [0.0, 0.0, 0.0]
 
         z_index = float(iz)
         y_index = float(iy)
@@ -378,10 +404,6 @@ def series_reconstruct_task(
         )
         return [float(pos[0]), float(pos[1]), float(pos[2])]
 
-    spacing_x = source_axis_spacings[src_x]
-    spacing_y = source_axis_spacings[src_y]
-    spacing_z = source_axis_spacings[src_z]
-
     def _reduce_slab(slab, reduce_axis=0):
         if recon_thickness_mode == "max":
             out = np.max(slab, axis=reduce_axis)
@@ -440,8 +462,8 @@ def series_reconstruct_task(
                 "pixel_spacing_out": [float(spacing_y), float(spacing_x)],
                 "spacing_between_slices_out": float(plane_spacing),
                 "slice_thickness_out": float(plane_thickness),
-                "image_orientation_out": [1.0, 0.0, 0.0, 0.0, 1.0, 0.0],
+                "image_orientation_out": _orientation_pair(patient_x_vec, patient_y_vec, patient_z_vec),
-                "plane_normal_out": [0.0, 0.0, 1.0],
+                "plane_normal_out": [float(patient_z_vec[0]), float(patient_z_vec[1]), float(patient_z_vec[2])],
                 "position_fn": lambda idx, centers=slab_centers_idx: position_from_patient_zyx(centers[idx], 0.0, 0.0),
             }
         elif plane_norm == "coronal":
@@ -452,13 +474,13 @@ def series_reconstruct_task(
             )
             plane_builders[plane_norm] = {
                 "count": int(len(slab_indices)),
-                "slice_fn": lambda idx, slabs=slab_indices: np.flipud(_reduce_slab(vol_zyx[:, slabs[idx], :], reduce_axis=1)),
+                "slice_fn": lambda idx, slabs=slab_indices: _reduce_slab(vol_zyx[:, slabs[idx], :], reduce_axis=1),
                 "pixel_spacing_out": [float(spacing_z), float(spacing_x)],
                 "spacing_between_slices_out": float(plane_spacing),
                 "slice_thickness_out": float(plane_thickness),
-                "image_orientation_out": [1.0, 0.0, 0.0, 0.0, 0.0, -1.0],
+                "image_orientation_out": _orientation_pair(patient_x_vec, patient_z_vec, patient_y_vec),
-                "plane_normal_out": [0.0, 1.0, 0.0],
+                "plane_normal_out": [float(patient_y_vec[0]), float(patient_y_vec[1]), float(patient_y_vec[2])],
-                "position_fn": lambda idx, centers=slab_centers_idx: position_from_patient_zyx(float(vol_zyx.shape[0] - 1), centers[idx], 0.0),
+                "position_fn": lambda idx, centers=slab_centers_idx: position_from_patient_zyx(0.0, centers[idx], 0.0),
             }
         elif plane_norm == "sagittal":
             plane_spacing = float(requested_slice_spacing) if requested_slice_spacing is not None else float(spacing_x)
@@ -468,13 +490,13 @@ def series_reconstruct_task(
             )
             plane_builders[plane_norm] = {
                 "count": int(len(slab_indices)),
-                "slice_fn": lambda idx, slabs=slab_indices: np.flipud(_reduce_slab(vol_zyx[:, :, slabs[idx]], reduce_axis=2)),
+                "slice_fn": lambda idx, slabs=slab_indices: _reduce_slab(vol_zyx[:, :, slabs[idx]], reduce_axis=2),
                 "pixel_spacing_out": [float(spacing_z), float(spacing_y)],
                 "spacing_between_slices_out": float(plane_spacing),
                 "slice_thickness_out": float(plane_thickness),
-                "image_orientation_out": [0.0, 1.0, 0.0, 0.0, 0.0, -1.0],
+                "image_orientation_out": _orientation_pair(patient_y_vec, patient_z_vec, patient_x_vec),
-                "plane_normal_out": [1.0, 0.0, 0.0],
+                "plane_normal_out": [float(patient_x_vec[0]), float(patient_x_vec[1]), float(patient_x_vec[2])],
-                "position_fn": lambda idx, centers=slab_centers_idx: position_from_patient_zyx(float(vol_zyx.shape[0] - 1), 0.0, centers[idx]),
+                "position_fn": lambda idx, centers=slab_centers_idx: position_from_patient_zyx(0.0, 0.0, centers[idx]),
             }
 
     if not plane_builders:

atlas/templates/atlas/series_reconstruct_advanced.html

@@ -33,7 +33,7 @@
         </div>
 
         <div class="alert alert-info recon-advanced-help">
-            <div><strong>Workflow:</strong> click <em>Apply MPR layout</em>, switch all panes to volume mode if needed, enable crosshairs in the DV3D toolbar, then position the crosshair planes as desired before generating reconstructions.</div>
+            <div><strong>Workflow:</strong> the page auto-configures a 3-volume MPR layout on load and attempts to enable crosshair-linked navigation. Adjust crosshairs as needed, then generate reconstructions.</div>
         </div>
 
         <div id="advanced_recon_root" class="dicom-viewer-root recon-advanced-viewer" data-images='{{ image_ids_json|safe }}'></div>
@@ -72,10 +72,11 @@
 
                     <div class="col-12 col-lg-4">
                         <label class="form-label" for="adv-recon-thickness">Slab thickness (mm)</label>
-                        <input id="adv-recon-thickness" type="number" step="0.1" min="0.1" name="recon_slice_thickness" class="form-control" placeholder="e.g. 2.5">
+                        <input id="adv-recon-thickness" type="number" step="0.1" min="0.1" name="recon_slice_thickness" class="form-control" value="3.0">
 
                         <label class="form-label mt-2" for="adv-recon-spacing">Slice spacing (mm)</label>
-                        <input id="adv-recon-spacing" type="number" step="0.1" min="0.1" name="recon_slice_spacing" class="form-control" placeholder="e.g. 1.0">
+                        <input id="adv-recon-spacing" type="number" step="0.1" min="3" name="recon_slice_spacing" class="form-control" value="3.0">
+                        <small class="text-muted d-block mt-1">Spacing is user-controlled and defaults to 3.0 mm minimum to reduce generated stack size.</small>
                     </div>
 
                     <div class="col-12 col-lg-4">
@@ -99,36 +100,176 @@
             </div>
         </div>
 
+        <div class="card border-0 shadow-sm mt-3">
+            <div class="card-body">
+                <div class="d-flex flex-wrap justify-content-between align-items-center gap-2 mb-2">
+                    <h6 class="mb-0">Live Reconstruction Plan</h6>
+                    <small id="advanced-plan-status" class="text-muted">Waiting for viewer telemetry...</small>
+                </div>
+                <div class="row g-2 small">
+                    <div class="col-12 col-md-4"><strong>Viewport 1:</strong> <span id="advanced-plan-vp0">-</span></div>
+                    <div class="col-12 col-md-4"><strong>Viewport 2:</strong> <span id="advanced-plan-vp1">-</span></div>
+                    <div class="col-12 col-md-4"><strong>Viewport 3:</strong> <span id="advanced-plan-vp2">-</span></div>
+                </div>
+                <div class="row g-2 small mt-1">
+                    <div class="col-12 col-md-6"><strong>Slab thickness:</strong> <span id="advanced-plan-thickness">3.0 mm</span></div>
+                    <div class="col-12 col-md-6"><strong>Slice spacing:</strong> <span id="advanced-plan-spacing">3.0 mm</span></div>
+                </div>
+            </div>
+        </div>
+
         <div id="advanced-recon-feedback" class="small mt-3"></div>
     </div>
 
     <script src="{% static 'dv3d/index.js' %}" type="module" defer="defer"></script>
     <script>
         (function () {
+            var ORIENTATION_LABELS = {
+                axial: 'Axial',
+                coronal: 'Coronal',
+                sagittal: 'Sagittal',
+            };
+
             function getViewerApi(name) {
                 return window[name + '_advanced_recon_root'] || window[name + '_advanced_recon'] || window[name + '_root'] || window[name];
             }
 
-            function buildMprState() {
+            function parseViewerState(raw) {
-                return {
+                if (!raw) {
+                    return null;
+                }
+                if (typeof raw === 'string') {
+                    try {
+                        return JSON.parse(raw);
+                    } catch (err) {
+                        return null;
+                    }
+                }
+                return raw;
+            }
+
+            function getDisplayOrientation(value) {
+                if (!value) {
+                    return 'Unknown';
+                }
+                return ORIENTATION_LABELS[value] || String(value).charAt(0).toUpperCase() + String(value).slice(1);
+            }
+
+            function ensureMprLayout() {
+                var exportFn = getViewerApi('exportViewerState');
+                var importFn = getViewerApi('importViewerState');
+                if (typeof importFn !== 'function') {
+                    return false;
+                }
+
+                var existing = parseViewerState(typeof exportFn === 'function' ? exportFn() : null) || {};
+                var stackIdx = Array.isArray(existing.stackIdx) ? existing.stackIdx : [];
+                var stacks = Array.isArray(existing.stacks) ? existing.stacks : [];
+                var baseStack = typeof stackIdx[0] === 'number' ? stackIdx[0] : (stacks.length > 0 ? 0 : null);
+
+                var nextState = {
                     grid: { rows: 1, cols: 3 },
                     modes: ['volume', 'volume', 'volume'],
                     orientations: ['axial', 'coronal', 'sagittal'],
                     volumeSliceIndices: [null, null, null],
                 };
+
+                if (stacks.length > 0 && baseStack !== null) {
+                    nextState.stacks = stacks;
+                    nextState.stackIdx = [baseStack, baseStack, baseStack];
+                }
+
+                try {
+                    importFn(nextState);
+                    return true;
+                } catch (err) {
+                    console.warn('Failed to apply automatic MPR layout', err);
+                    return false;
+                }
+            }
+
+            function tryEnableCrosshairs() {
+                var labels = ['Enable Cross Reference Lines', 'Enable Crosshairs'];
+                var root = document.getElementById('advanced_recon_root');
+                var scope = root ? root.parentElement || document : document;
+                var buttons = scope.querySelectorAll('button');
+                var clicked = false;
+
+                buttons.forEach(function (btn) {
+                    if (clicked) {
+                        return;
+                    }
+                    var text = (btn.textContent || '').trim();
+                    if (!text) {
+                        return;
+                    }
+                    for (var i = 0; i < labels.length; i++) {
+                        if (text.indexOf(labels[i]) !== -1) {
+                            btn.click();
+                            clicked = true;
+                            break;
+                        }
+                    }
+                });
+
+                return clicked;
+            }
+
+            function formatViewportPlan(state, idx) {
+                if (!state) {
+                    return '-';
+                }
+                var modes = Array.isArray(state.modes) ? state.modes : [];
+                var orientations = Array.isArray(state.orientations) ? state.orientations : [];
+                var slices = Array.isArray(state.volumeSliceIndices) ? state.volumeSliceIndices : [];
+                var mode = modes[idx] || 'unknown';
+                var orientation = getDisplayOrientation(orientations[idx]);
+                var slice = slices[idx];
+                var sliceText = typeof slice === 'number' ? ('slice ' + slice) : 'slice n/a';
+                return orientation + ' (' + mode + ', ' + sliceText + ')';
+            }
+
+            function updateLivePlan() {
+                var exportFn = getViewerApi('exportViewerState');
+                var thicknessInput = document.getElementById('adv-recon-thickness');
+                var spacingInput = document.getElementById('adv-recon-spacing');
+                var state = parseViewerState(typeof exportFn === 'function' ? exportFn() : null);
+
+                var statusEl = document.getElementById('advanced-plan-status');
+                var vp0 = document.getElementById('advanced-plan-vp0');
+                var vp1 = document.getElementById('advanced-plan-vp1');
+                var vp2 = document.getElementById('advanced-plan-vp2');
+                var thicknessEl = document.getElementById('advanced-plan-thickness');
+                var spacingEl = document.getElementById('advanced-plan-spacing');
+
+                if (statusEl) {
+                    statusEl.textContent = state ? 'Viewer telemetry active' : 'Waiting for viewer telemetry...';
+                }
+                if (vp0) {
+                    vp0.textContent = formatViewportPlan(state, 0);
+                }
+                if (vp1) {
+                    vp1.textContent = formatViewportPlan(state, 1);
+                }
+                if (vp2) {
+                    vp2.textContent = formatViewportPlan(state, 2);
+                }
+
+                if (thicknessEl) {
+                    var thicknessValue = thicknessInput && thicknessInput.value ? thicknessInput.value : '3.0';
+                    thicknessEl.textContent = thicknessValue + ' mm';
+                }
+                if (spacingEl) {
+                    var spacingValue = spacingInput && spacingInput.value ? spacingInput.value : '3.0';
+                    spacingEl.textContent = spacingValue + ' mm';
+                }
             }
 
             var applyBtn = document.getElementById('apply-mpr-layout');
             if (applyBtn) {
                 applyBtn.addEventListener('click', function () {
-                    var importFn = getViewerApi('importViewerState');
+                    ensureMprLayout();
-                    if (typeof importFn === 'function') {
+                    setTimeout(updateLivePlan, 400);
-                        try {
-                            importFn(buildMprState());
-                        } catch (err) {
-                            console.warn('Failed to apply MPR layout', err);
-                        }
-                    }
                 });
             }
 
@@ -150,6 +291,30 @@
                     }
                 });
             }
+
+            var thicknessInput = document.getElementById('adv-recon-thickness');
+            var spacingInput = document.getElementById('adv-recon-spacing');
+            if (thicknessInput) {
+                thicknessInput.addEventListener('input', updateLivePlan);
+            }
+            if (spacingInput) {
+                spacingInput.addEventListener('input', updateLivePlan);
+            }
+
+            var autoAttempts = 0;
+            var autoTimer = setInterval(function () {
+                autoAttempts += 1;
+                var mprApplied = ensureMprLayout();
+                var crosshairEnabled = tryEnableCrosshairs();
+                updateLivePlan();
+
+                if ((mprApplied && crosshairEnabled) || autoAttempts >= 12) {
+                    clearInterval(autoTimer);
+                }
+            }, 600);
+
+            setInterval(updateLivePlan, 700);
+            setTimeout(updateLivePlan, 1500);
         })();
     </script>
 {% endblock %}