From 1c76e0696c00e2df324609041c3842f35b8bf7c0 Mon Sep 17 00:00:00 2001 From: Ross Date: Mon, 18 May 2026 07:48:24 +0100 Subject: [PATCH] feat(tasks): Refactor series_reconstruct_task and add _stamp_derived_dataset for improved dataset handling --- atlas/tasks.py | 20 ++---- atlas/templates/atlas/series_viewer.html | 4 +- atlas/views.py | 83 ++++++++++++++++++++++-- 3 files changed, 88 insertions(+), 19 deletions(-) diff --git a/atlas/tasks.py b/atlas/tasks.py index e752705d..d312269e 100644 --- a/atlas/tasks.py +++ b/atlas/tasks.py @@ -86,7 +86,6 @@ from generic.models import CimarCase from rad.settings import REMOTE_URL, CIMAR_USERNAME, CIMAR_PASSWORD from helpers.cimar import CimarAPI, NotFoundError from pydicom.uid import generate_uid -from datetime import datetime from django.contrib.auth.models import User from django.core.files.base import ContentFile from django.core.cache import cache @@ -392,9 +391,6 @@ def series_reconstruct_task( recon_series = atlas_views._create_series_derivative(series, f"Recon {plane_norm.title()} ({source_plane.title()} src)") recon_series.series_instance_uid = generate_uid() recon_series.save(update_fields=["series_instance_uid"]) - now = datetime.utcnow() - date_str = now.strftime("%Y%m%d") - time_str = now.strftime("%H%M%S.%f")[:13] for idx in range(int(cfg["count"])): arr2d = cfg["slice_fn"](idx) @@ -404,18 +400,16 @@ def series_reconstruct_task( ds_new.Rows = int(arr2d.shape[0]) ds_new.Columns = int(arr2d.shape[1]) ds_new.InstanceNumber = idx + 1 - ds_new.SOPInstanceUID = generate_uid() - ds_new.SeriesInstanceUID = recon_series.series_instance_uid - ds_new.SeriesDescription = recon_series.description or f"Recon {plane_norm.title()}" - ds_new.ImageType = ["DERIVED", "SECONDARY", "MPR"] - ds_new.DerivationDescription = ( + atlas_views._stamp_derived_dataset( + ds_new, + series_instance_uid=recon_series.series_instance_uid, + series_description=recon_series.description or f"Recon {plane_norm.title()}", + derivation_description=( f"{plane_norm.title()} reconstruction; mode={recon_thickness_mode}; " f"thickness={float(cfg['slice_thickness_out']):.3f}mm; spacing={float(cfg['spacing_between_slices_out']):.3f}mm" + ), + image_type=["DERIVED", "SECONDARY", "MPR"], ) - ds_new.ContentDate = date_str - ds_new.ContentTime = time_str - ds_new.InstanceCreationDate = date_str - ds_new.InstanceCreationTime = time_str ds_new.PixelData = arr2d.tobytes() ds_new.PixelSpacing = [float(cfg["pixel_spacing_out"][0]), float(cfg["pixel_spacing_out"][1])] ds_new.ImageOrientationPatient = cfg["image_orientation_out"] diff --git a/atlas/templates/atlas/series_viewer.html b/atlas/templates/atlas/series_viewer.html index d2331315..f41155a8 100755 --- a/atlas/templates/atlas/series_viewer.html +++ b/atlas/templates/atlas/series_viewer.html @@ -212,7 +212,7 @@
@@ -255,7 +255,7 @@
-
Series Optimization
+
Series Tools
diff --git a/atlas/views.py b/atlas/views.py index 63833bd7..b02c4de4 100755 --- a/atlas/views.py +++ b/atlas/views.py @@ -307,7 +307,45 @@ def _resize_array_nearest(arr, target_rows, target_cols): return arr[np.ix_(row_idx, col_idx)] -def _downsample_dicom_dataset(ds, reduction_pct): +def _stamp_derived_dataset( + ds, + *, + series_instance_uid=None, + series_description=None, + derivation_description=None, + image_type=None, + regenerate_sop_instance_uid=True, + stamp_series_datetime=True, +): + now = timezone.now() + date_str = now.strftime("%Y%m%d") + time_str = now.strftime("%H%M%S.%f")[:13] + + if regenerate_sop_instance_uid: + ds.SOPInstanceUID = generate_uid() + if series_instance_uid: + ds.SeriesInstanceUID = series_instance_uid + if series_description: + ds.SeriesDescription = series_description + + ds.ImageType = image_type or ["DERIVED", "SECONDARY"] + + if derivation_description: + ds.DerivationDescription = derivation_description + + ds.ContentDate = date_str + ds.ContentTime = time_str + ds.InstanceCreationDate = date_str + ds.InstanceCreationTime = time_str + + if stamp_series_datetime: + ds.SeriesDate = date_str + ds.SeriesTime = time_str + + return ds + + +def _downsample_dicom_dataset(ds, reduction_pct, *, series_instance_uid=None, series_description=None): if reduction_pct <= 0 or reduction_pct >= 100: raise ValueError("Downsample percentage must be between 1 and 99") @@ -321,11 +359,36 @@ def _downsample_dicom_dataset(ds, reduction_pct): target_cols = max(1, int(round(px.shape[1] * factor))) resized = _resize_array_nearest(px, target_rows, target_cols) + derivation_description = f"Downsampled by {reduction_pct}% using nearest-neighbour resize" + _stamp_derived_dataset( + ds, + series_instance_uid=series_instance_uid, + series_description=series_description, + derivation_description=derivation_description, + image_type=["DERIVED", "SECONDARY"], + ) + + if hasattr(ds, "PixelSpacing") and ds.PixelSpacing and len(ds.PixelSpacing) >= 2: + row_spacing = _safe_float(ds.PixelSpacing[0], 1.0) + col_spacing = _safe_float(ds.PixelSpacing[1], 1.0) + ds.PixelSpacing = [float(row_spacing / factor), float(col_spacing / factor)] + + if hasattr(ds, "ImagerPixelSpacing") and ds.ImagerPixelSpacing and len(ds.ImagerPixelSpacing) >= 2: + row_spacing = _safe_float(ds.ImagerPixelSpacing[0], 1.0) + col_spacing = _safe_float(ds.ImagerPixelSpacing[1], 1.0) + ds.ImagerPixelSpacing = [float(row_spacing / factor), float(col_spacing / factor)] + + if hasattr(ds, "NominalScannedPixelSpacing") and ds.NominalScannedPixelSpacing and len(ds.NominalScannedPixelSpacing) >= 2: + row_spacing = _safe_float(ds.NominalScannedPixelSpacing[0], 1.0) + col_spacing = _safe_float(ds.NominalScannedPixelSpacing[1], 1.0) + ds.NominalScannedPixelSpacing = [float(row_spacing / factor), float(col_spacing / factor)] + ds.Rows = int(target_rows) ds.Columns = int(target_cols) ds.PixelData = resized.tobytes() ds.pop("SmallestImagePixelValue", None) ds.pop("LargestImagePixelValue", None) + ds.pop("PixelAspectRatio", None) return ds @@ -606,7 +669,12 @@ def series_optimize_htmx(request, series_id): continue try: - ds_out = _downsample_dicom_dataset(ds, downsample_pct) + ds_out = _downsample_dicom_dataset( + ds, + downsample_pct, + series_instance_uid=preview_series.series_instance_uid, + series_description=preview_series.description, + ) except Exception as exc: logger.warning("Downsample preview failed for image {}: {}", image.pk, exc) continue @@ -645,6 +713,7 @@ def series_optimize_htmx(request, series_id): ) downsampled = [] + replacement_series_uid = generate_uid() for image in full_series_images: ds = _read_series_image_dataset(image) if ds is None: @@ -652,7 +721,12 @@ def series_optimize_htmx(request, series_id): try: original_hash = image.image_blake3_hash - ds_out = _downsample_dicom_dataset(ds, downsample_pct) + ds_out = _downsample_dicom_dataset( + ds, + downsample_pct, + series_instance_uid=replacement_series_uid, + series_description=series.description, + ) out_io = io.BytesIO() ds_out.save_as(out_io, write_like_original=False) out_io.seek(0) @@ -671,7 +745,8 @@ def series_optimize_htmx(request, series_id): if downsampled: series.modified = Series.SeriesModifiedChocies.RE - series.save(update_fields=["modified"]) + series.series_instance_uid = replacement_series_uid + series.save(update_fields=["modified", "series_instance_uid"]) return HttpResponse( f'
Downsample complete ({downsample_pct}%). Updated {len(downsampled)} images while preserving original hashes.
'