try to fix recons
This commit is contained in:
Ross
+37
-15
@@ -336,6 +336,32 @@ def series_reconstruct_task(
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src_y = source_for_patient_axis[1]
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src_z = source_for_patient_axis[2]
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# Build patient-axis basis vectors expressed in source/world space.
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# This preserves source world-frame orientation (including obliquity/sign)
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# for derived series instead of hardcoding cardinal axes.
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patient_x_vec = np.asarray(source_axis_dirs[src_x], dtype=float) * float(sign_for_patient_axis[0])
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patient_y_vec = np.asarray(source_axis_dirs[src_y], dtype=float) * float(sign_for_patient_axis[1])
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patient_z_vec = np.asarray(source_axis_dirs[src_z], dtype=float) * float(sign_for_patient_axis[2])
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def _norm_vec(vec):
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nrm = float(np.linalg.norm(vec))
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if nrm == 0:
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return np.asarray(vec, dtype=float)
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return np.asarray(vec, dtype=float) / nrm
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patient_x_vec = _norm_vec(patient_x_vec)
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patient_y_vec = _norm_vec(patient_y_vec)
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patient_z_vec = _norm_vec(patient_z_vec)
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def _orientation_pair(col_vec, row_vec, desired_normal):
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col = _norm_vec(col_vec)
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row = _norm_vec(row_vec)
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desired = _norm_vec(desired_normal)
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normal = np.cross(col, row)
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if float(np.dot(normal, desired)) < 0:
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row = -row
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return [float(col[0]), float(col[1]), float(col[2]), float(row[0]), float(row[1]), float(row[2])]
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spacing_x = source_axis_spacings[src_x]
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spacing_y = source_axis_spacings[src_y]
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spacing_z = source_axis_spacings[src_z]
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@@ -350,7 +376,7 @@ def series_reconstruct_task(
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vol_zyx = np.flip(vol_zyx, axis=2)
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def source_indices_from_patient_zyx(iz, iy, ix):
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src_indices = [0, 0, 0]
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src_indices = [0.0, 0.0, 0.0]
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z_index = float(iz)
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y_index = float(iy)
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@@ -378,10 +404,6 @@ def series_reconstruct_task(
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)
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return [float(pos[0]), float(pos[1]), float(pos[2])]
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spacing_x = source_axis_spacings[src_x]
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spacing_y = source_axis_spacings[src_y]
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spacing_z = source_axis_spacings[src_z]
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def _reduce_slab(slab, reduce_axis=0):
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if recon_thickness_mode == "max":
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out = np.max(slab, axis=reduce_axis)
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@@ -440,8 +462,8 @@ def series_reconstruct_task(
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"pixel_spacing_out": [float(spacing_y), float(spacing_x)],
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"spacing_between_slices_out": float(plane_spacing),
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"slice_thickness_out": float(plane_thickness),
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"image_orientation_out": [1.0, 0.0, 0.0, 0.0, 1.0, 0.0],
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"plane_normal_out": [0.0, 0.0, 1.0],
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"image_orientation_out": _orientation_pair(patient_x_vec, patient_y_vec, patient_z_vec),
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"plane_normal_out": [float(patient_z_vec[0]), float(patient_z_vec[1]), float(patient_z_vec[2])],
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"position_fn": lambda idx, centers=slab_centers_idx: position_from_patient_zyx(centers[idx], 0.0, 0.0),
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}
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elif plane_norm == "coronal":
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@@ -452,13 +474,13 @@ def series_reconstruct_task(
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)
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plane_builders[plane_norm] = {
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"count": int(len(slab_indices)),
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"slice_fn": lambda idx, slabs=slab_indices: np.flipud(_reduce_slab(vol_zyx[:, slabs[idx], :], reduce_axis=1)),
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"slice_fn": lambda idx, slabs=slab_indices: _reduce_slab(vol_zyx[:, slabs[idx], :], reduce_axis=1),
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"pixel_spacing_out": [float(spacing_z), float(spacing_x)],
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"spacing_between_slices_out": float(plane_spacing),
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"slice_thickness_out": float(plane_thickness),
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"image_orientation_out": [1.0, 0.0, 0.0, 0.0, 0.0, -1.0],
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"plane_normal_out": [0.0, 1.0, 0.0],
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"position_fn": lambda idx, centers=slab_centers_idx: position_from_patient_zyx(float(vol_zyx.shape[0] - 1), centers[idx], 0.0),
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"image_orientation_out": _orientation_pair(patient_x_vec, patient_z_vec, patient_y_vec),
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"plane_normal_out": [float(patient_y_vec[0]), float(patient_y_vec[1]), float(patient_y_vec[2])],
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"position_fn": lambda idx, centers=slab_centers_idx: position_from_patient_zyx(0.0, centers[idx], 0.0),
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}
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elif plane_norm == "sagittal":
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plane_spacing = float(requested_slice_spacing) if requested_slice_spacing is not None else float(spacing_x)
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@@ -468,13 +490,13 @@ def series_reconstruct_task(
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)
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plane_builders[plane_norm] = {
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"count": int(len(slab_indices)),
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"slice_fn": lambda idx, slabs=slab_indices: np.flipud(_reduce_slab(vol_zyx[:, :, slabs[idx]], reduce_axis=2)),
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"slice_fn": lambda idx, slabs=slab_indices: _reduce_slab(vol_zyx[:, :, slabs[idx]], reduce_axis=2),
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"pixel_spacing_out": [float(spacing_z), float(spacing_y)],
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"spacing_between_slices_out": float(plane_spacing),
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"slice_thickness_out": float(plane_thickness),
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"image_orientation_out": [0.0, 1.0, 0.0, 0.0, 0.0, -1.0],
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"plane_normal_out": [1.0, 0.0, 0.0],
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"position_fn": lambda idx, centers=slab_centers_idx: position_from_patient_zyx(float(vol_zyx.shape[0] - 1), 0.0, centers[idx]),
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"image_orientation_out": _orientation_pair(patient_y_vec, patient_z_vec, patient_x_vec),
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"plane_normal_out": [float(patient_x_vec[0]), float(patient_x_vec[1]), float(patient_x_vec[2])],
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"position_fn": lambda idx, centers=slab_centers_idx: position_from_patient_zyx(0.0, 0.0, centers[idx]),
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}
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if not plane_builders:
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@@ -33,7 +33,7 @@
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</div>
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<div class="alert alert-info recon-advanced-help">
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<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>
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<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>
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</div>
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<div id="advanced_recon_root" class="dicom-viewer-root recon-advanced-viewer" data-images='{{ image_ids_json|safe }}'></div>
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@@ -72,10 +72,11 @@
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<div class="col-12 col-lg-4">
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<label class="form-label" for="adv-recon-thickness">Slab thickness (mm)</label>
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<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">
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<input id="adv-recon-thickness" type="number" step="0.1" min="0.1" name="recon_slice_thickness" class="form-control" value="3.0">
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<label class="form-label mt-2" for="adv-recon-spacing">Slice spacing (mm)</label>
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<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">
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<input id="adv-recon-spacing" type="number" step="0.1" min="3" name="recon_slice_spacing" class="form-control" value="3.0">
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<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>
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</div>
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<div class="col-12 col-lg-4">
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@@ -99,36 +100,176 @@
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</div>
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</div>
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<div class="card border-0 shadow-sm mt-3">
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<div class="card-body">
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<div class="d-flex flex-wrap justify-content-between align-items-center gap-2 mb-2">
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<h6 class="mb-0">Live Reconstruction Plan</h6>
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<small id="advanced-plan-status" class="text-muted">Waiting for viewer telemetry...</small>
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</div>
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<div class="row g-2 small">
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<div class="col-12 col-md-4"><strong>Viewport 1:</strong> <span id="advanced-plan-vp0">-</span></div>
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<div class="col-12 col-md-4"><strong>Viewport 2:</strong> <span id="advanced-plan-vp1">-</span></div>
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<div class="col-12 col-md-4"><strong>Viewport 3:</strong> <span id="advanced-plan-vp2">-</span></div>
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</div>
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<div class="row g-2 small mt-1">
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<div class="col-12 col-md-6"><strong>Slab thickness:</strong> <span id="advanced-plan-thickness">3.0 mm</span></div>
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<div class="col-12 col-md-6"><strong>Slice spacing:</strong> <span id="advanced-plan-spacing">3.0 mm</span></div>
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</div>
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</div>
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</div>
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<div id="advanced-recon-feedback" class="small mt-3"></div>
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</div>
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<script src="{% static 'dv3d/index.js' %}" type="module" defer="defer"></script>
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<script>
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(function () {
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var ORIENTATION_LABELS = {
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axial: 'Axial',
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coronal: 'Coronal',
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sagittal: 'Sagittal',
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};
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function getViewerApi(name) {
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return window[name + '_advanced_recon_root'] || window[name + '_advanced_recon'] || window[name + '_root'] || window[name];
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}
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function buildMprState() {
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return {
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function parseViewerState(raw) {
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if (!raw) {
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return null;
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}
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if (typeof raw === 'string') {
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try {
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return JSON.parse(raw);
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} catch (err) {
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return null;
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}
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}
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return raw;
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}
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function getDisplayOrientation(value) {
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if (!value) {
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return 'Unknown';
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}
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return ORIENTATION_LABELS[value] || String(value).charAt(0).toUpperCase() + String(value).slice(1);
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}
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function ensureMprLayout() {
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var exportFn = getViewerApi('exportViewerState');
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var importFn = getViewerApi('importViewerState');
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if (typeof importFn !== 'function') {
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return false;
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}
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var existing = parseViewerState(typeof exportFn === 'function' ? exportFn() : null) || {};
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var stackIdx = Array.isArray(existing.stackIdx) ? existing.stackIdx : [];
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var stacks = Array.isArray(existing.stacks) ? existing.stacks : [];
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var baseStack = typeof stackIdx[0] === 'number' ? stackIdx[0] : (stacks.length > 0 ? 0 : null);
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var nextState = {
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grid: { rows: 1, cols: 3 },
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modes: ['volume', 'volume', 'volume'],
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orientations: ['axial', 'coronal', 'sagittal'],
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volumeSliceIndices: [null, null, null],
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};
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if (stacks.length > 0 && baseStack !== null) {
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nextState.stacks = stacks;
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nextState.stackIdx = [baseStack, baseStack, baseStack];
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}
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try {
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importFn(nextState);
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return true;
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} catch (err) {
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console.warn('Failed to apply automatic MPR layout', err);
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return false;
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}
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}
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function tryEnableCrosshairs() {
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var labels = ['Enable Cross Reference Lines', 'Enable Crosshairs'];
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var root = document.getElementById('advanced_recon_root');
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var scope = root ? root.parentElement || document : document;
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var buttons = scope.querySelectorAll('button');
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var clicked = false;
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buttons.forEach(function (btn) {
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if (clicked) {
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return;
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}
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var text = (btn.textContent || '').trim();
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if (!text) {
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return;
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}
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for (var i = 0; i < labels.length; i++) {
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if (text.indexOf(labels[i]) !== -1) {
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btn.click();
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clicked = true;
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break;
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}
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}
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});
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return clicked;
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}
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function formatViewportPlan(state, idx) {
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if (!state) {
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return '-';
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}
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var modes = Array.isArray(state.modes) ? state.modes : [];
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var orientations = Array.isArray(state.orientations) ? state.orientations : [];
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var slices = Array.isArray(state.volumeSliceIndices) ? state.volumeSliceIndices : [];
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var mode = modes[idx] || 'unknown';
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var orientation = getDisplayOrientation(orientations[idx]);
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var slice = slices[idx];
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var sliceText = typeof slice === 'number' ? ('slice ' + slice) : 'slice n/a';
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return orientation + ' (' + mode + ', ' + sliceText + ')';
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}
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function updateLivePlan() {
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var exportFn = getViewerApi('exportViewerState');
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var thicknessInput = document.getElementById('adv-recon-thickness');
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var spacingInput = document.getElementById('adv-recon-spacing');
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var state = parseViewerState(typeof exportFn === 'function' ? exportFn() : null);
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var statusEl = document.getElementById('advanced-plan-status');
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var vp0 = document.getElementById('advanced-plan-vp0');
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var vp1 = document.getElementById('advanced-plan-vp1');
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var vp2 = document.getElementById('advanced-plan-vp2');
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var thicknessEl = document.getElementById('advanced-plan-thickness');
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var spacingEl = document.getElementById('advanced-plan-spacing');
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if (statusEl) {
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statusEl.textContent = state ? 'Viewer telemetry active' : 'Waiting for viewer telemetry...';
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}
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if (vp0) {
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vp0.textContent = formatViewportPlan(state, 0);
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}
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if (vp1) {
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vp1.textContent = formatViewportPlan(state, 1);
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}
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if (vp2) {
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vp2.textContent = formatViewportPlan(state, 2);
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}
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if (thicknessEl) {
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var thicknessValue = thicknessInput && thicknessInput.value ? thicknessInput.value : '3.0';
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thicknessEl.textContent = thicknessValue + ' mm';
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}
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if (spacingEl) {
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var spacingValue = spacingInput && spacingInput.value ? spacingInput.value : '3.0';
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spacingEl.textContent = spacingValue + ' mm';
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}
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}
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var applyBtn = document.getElementById('apply-mpr-layout');
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if (applyBtn) {
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applyBtn.addEventListener('click', function () {
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var importFn = getViewerApi('importViewerState');
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if (typeof importFn === 'function') {
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try {
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importFn(buildMprState());
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} catch (err) {
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console.warn('Failed to apply MPR layout', err);
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}
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}
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ensureMprLayout();
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setTimeout(updateLivePlan, 400);
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});
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}
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@@ -150,6 +291,30 @@
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}
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});
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}
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var thicknessInput = document.getElementById('adv-recon-thickness');
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var spacingInput = document.getElementById('adv-recon-spacing');
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if (thicknessInput) {
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thicknessInput.addEventListener('input', updateLivePlan);
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}
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if (spacingInput) {
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spacingInput.addEventListener('input', updateLivePlan);
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}
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var autoAttempts = 0;
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var autoTimer = setInterval(function () {
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autoAttempts += 1;
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var mprApplied = ensureMprLayout();
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var crosshairEnabled = tryEnableCrosshairs();
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updateLivePlan();
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if ((mprApplied && crosshairEnabled) || autoAttempts >= 12) {
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clearInterval(autoTimer);
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}
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}, 600);
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setInterval(updateLivePlan, 700);
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setTimeout(updateLivePlan, 1500);
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})();
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</script>
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{% endblock %}
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Reference in New Issue
Block a user