update main workflow

dask-stitch/scripts/create_test_dataset_singletile.py

@@ -7,7 +7,7 @@
 import math
 from zarrnii import ZarrNii
 
-def create_test_dataset_single(tile_index, template="MNI152NLin2009cAsym", res=2, grid_shape=(3, 4), overlap=16, random_seed=42, final_chunks=(1,32, 32, 1)):
+def create_test_dataset_single(tile_index, template="MNI152NLin2009cAsym", res=2, grid_shape=(3, 4), overlap=16, random_seed=42, final_chunks=(1,32, 32, 32)):
     """
     Create a low-resolution test dataset for tile-based stitching.
 

dask-stitch/scripts/fuse_volume.py

@@ -1,5 +1,5 @@
 from lib.utils import *
-
+from zarrnii import ZarrNii
 
 # Paths to input tiles
 ome_zarr_paths = snakemake.input.ome_zarr
@@ -9,46 +9,20 @@
 
 
 # Parameters for the fused array
-fused_shape = (128,128,128)  # Full shape of the fused array
-chunk_shape = (64,64,64)  # Chunk size of the fused array
-global_bbox_min = np.array([0, 0, 0])  # Minimum physical coordinate of the fused array
-target_voxel_spacing = np.array([1.0, 1.0, 1.0])  # Voxel spacing of the fused array
-
-# Create an empty Dask array for the fused output
-fused_dask_array = da.zeros(fused_shape, chunks=chunk_shape, dtype=np.float32)
-
-
-
-# Apply map_blocks to process the fused array
-processed_dask_array = fused_dask_array.map_blocks(
-    process_block,
-    dtype=np.float32,
-    rtree_idx=rtree_idx,
-    znimgs=znimgs,
-    global_bbox_min=global_bbox_min,
-    target_voxel_spacing=target_voxel_spacing,
-)
-
+output_shape=(400,400,400)
+output_chunks=(100,100,100)
+fused_dask_array = da.zeros(output_shape, chunks=output_chunks, dtype=np.float32)
+znimg_out = ZarrNii.from_darr(fused_dask_array,
+                                             axes_order=znimgs[0].axes_order,
+                                             orientation=znimgs[0].get_orientation(),
+                                             spacing=(1,1,1),
+                                             origin=(-100,-100,-100))
 
-znimg_out = ZarrNii.from_darr(processed_dask_array.reshape((1,processed_dask_array.shape[0],processed_dask_array.shape[1],processed_dask_array.shape[2])))
-znimg_out.to_ome_zarr(snakemake.output.ome_zarr)
-znimg_out.to_nifti(snakemake.output.nifti)
+znimg_fused = fuse_output_blocks(znimg_out,rtree_idx=rtree_idx,tile_znimgs=znimgs)
 
-"""
+znimg_fused.to_ome_zarr(snakemake.output.ome_zarr)
 
-print('doing test query')
-# Define the bounding box of an output chunk (example)
-output_chunk_bbox =( -1, -1, -1, 0,0,0)  # Replace with actual bounding box of a fused chunk
-output_chunk_bbox =( -36, -33, -49, -35,-32,-47)  # Replace with actual bounding box of a fused chunk
-print(output_chunk_bbox)
+ZarrNii.from_ome_zarr(snakemake.output.ome_zarr).to_nifti(snakemake.output.nifti)
 
-# Query intersecting chunks
-intersecting_chunks = query_intersections(rtree_idx, output_chunk_bbox)
 
-print(f'found {len(intersecting_chunks)} chunks')
-# Extract the attached data (tile_idx, chunk_id)
-for entry in intersecting_chunks:
-    tile_idx, chunk_id = entry.object
-    print(f"Intersecting chunk: tile_idx={tile_idx}, chunk_id={chunk_id}")
 
-"""