siibra 1.0a8__py3-none-any.whl → 1.0a11__py3-none-any.whl

siibra/volumes/providers/neuroglancer.py

@@ -15,7 +15,14 @@
 
 from . import provider as _provider
 
-from ...commons import logger, MapType, merge_meshes, SIIBRA_MAX_FETCH_SIZE_GIB
+from ...commons import (
+    logger,
+    MapType,
+    merge_meshes,
+    SIIBRA_MAX_FETCH_SIZE_GIB,
+    QUIET,
+    resample_img_to_img
+)
 from ...retrieval import requests, cache
 from ...locations import boundingbox as _boundingbox
 
@@ -86,10 +93,11 @@ class NeuroglancerProvider(_provider.VolumeProvider, srctype="neuroglancer/preco
 
         if len(self._fragments) > 1:
             if fragment is None:
-                raise RuntimeError(
-                    f"Merging of fragments not yet implemented in {self.__class__.__name__}. "
-                    f"Specify one of [{', '.join(self._fragments.keys())}] using fetch(fragment=<name>). "
+                logger.info(
+                    f"Merging fragments [{', '.join(self._fragments.keys())}]. "
+                    f"You can select one using `fragment` kwarg."
                 )
+                result = self._merge_fragments(resolution_mm=resolution_mm, voi=voi, **kwargs)
             else:
                 matched_names = [n for n in self._fragments if fragment.lower() in n.lower()]
                 if len(matched_names) != 1:
@@ -157,45 +165,67 @@ class NeuroglancerProvider(_provider.VolumeProvider, srctype="neuroglancer/preco
                     np.asanyarray(img.dataobj), threshold=background, space=None
                 ).transform(img.affine)  # use the affine of the image matching fetch_kwargs
             else:
-                shape = frag.shape[:3]
+                resolution_mm = fetch_kwargs.get("resolution_mm")
+                if resolution_mm is None:
+                    affine = frag.affine
+                    shape = frag.shape[:3]
+                else:
+                    scale = frag._select_scale(resolution_mm=resolution_mm)
+                    affine = scale.affine
+                    shape = scale.size[:3]
                 next_bbox = _boundingbox.BoundingBox(
                     (0, 0, 0), shape, space=None
-                ).transform(frag.affine)
+                ).transform(affine)
             bbox = next_bbox if bbox is None else bbox.union(next_bbox)
         return bbox
 
-    def _merge_fragments(self) -> nib.Nifti1Image:
-        # TODO this only performs nearest neighbor interpolation, optimized for float types.
-        bbox = self.get_boundingbox(clip=False, background=0.0)
+    def _merge_fragments(
+        self,
+        resolution_mm: float = None,
+        voi: _boundingbox.BoundingBox = None,
+        **kwargs
+    ) -> nib.Nifti1Image:
+        with QUIET:
+            bbox = self.get_boundingbox(
+                clip=False,
+                background=0,
+                resolution_mm=resolution_mm,
+                voi=voi
+            )
+
         num_conflicts = 0
         result = None
-
-        for loader in self._img_loaders.values():
-            img = loader()
+        for frag_vol in self._fragments.values():
+            frag_scale = frag_vol._select_scale(
+                resolution_mm=resolution_mm,
+                bbox=voi,
+                max_bytes=kwargs.pop("maxbytes", NeuroglancerVolume.MAX_BYTES)
+            )
+            img = frag_scale.fetch(voi=voi)
             if result is None:
                 # build the empty result image with its own affine and voxel space
                 s0 = np.identity(4)
                 s0[:3, -1] = list(bbox.minpoint.transform(np.linalg.inv(img.affine)))
                 result_affine = np.dot(img.affine, s0)  # adjust global bounding box offset to get global affine
-                voxdims = np.asanyarray(bbox.transform(result_affine).shape, dtype="int")
+                voxdims = np.asanyarray(np.ceil(
+                    bbox.transform(np.linalg.inv(result_affine)).shape  # transform to the voxel space
+                ), dtype="int")
                 result_arr = np.zeros(voxdims, dtype=img.dataobj.dtype)
                 result = nib.Nifti1Image(dataobj=result_arr, affine=result_affine)
 
-            arr = np.asanyarray(img.dataobj)
-            Xs, Ys, Zs = np.where(arr != 0)
-            Xt, Yt, Zt, _ = np.split(
-                (np.dot(
-                    np.linalg.inv(result_affine),
-                    np.dot(img.affine, np.c_[Xs, Ys, Zs, Zs * 0 + 1].T)
-                ) + .5).astype('int'),
-                4, axis=0
-            )
-            num_conflicts += np.count_nonzero(result_arr[Xt, Yt, Zt])
-            result_arr[Xt, Yt, Zt] = arr[Xs, Ys, Zs]
+            # resample to merge template and update it
+            resampled_img = resample_img_to_img(source_img=img, target_img=result)
+            arr = np.asanyarray(resampled_img.dataobj)
+            nonzero_voxels = arr != 0
+            num_conflicts += np.count_nonzero(result_arr[nonzero_voxels])
+            result_arr[nonzero_voxels] = arr[nonzero_voxels]
 
         if num_conflicts > 0:
             num_voxels = np.count_nonzero(result_arr)
-            logger.warning(f"Merging fragments required to overwrite {num_conflicts} conflicting voxels ({num_conflicts/num_voxels*100.:2.1f}%).")
+            logger.warning(
+                f"Merging fragments required to overwrite {num_conflicts} "
+                f"conflicting voxels ({num_conflicts / num_voxels * 100.:2.3f}%)."
+            )
 
         return result
 

siibra/volumes/providers/nifti.py

@@ -15,7 +15,7 @@
 
 from . import provider as _provider
 
-from ...commons import logger
+from ...commons import logger, resample_img_to_img
 from ...retrieval import requests
 from ...locations import pointset, boundingbox as _boundingbox
 
@@ -108,11 +108,9 @@ class NiftiProvider(_provider.VolumeProvider, srctype="nii"):
         return bbox
 
     def _merge_fragments(self) -> nib.Nifti1Image:
-        # TODO this only performs nearest neighbor interpolation, optimized for float types.
         bbox = self.get_boundingbox(clip=False, background=0.0)
         num_conflicts = 0
         result = None
-
         for loader in self._img_loaders.values():
             img = loader()
             if result is None:
@@ -120,25 +118,25 @@ class NiftiProvider(_provider.VolumeProvider, srctype="nii"):
                 s0 = np.identity(4)
                 s0[:3, -1] = list(bbox.minpoint.transform(np.linalg.inv(img.affine)))
                 result_affine = np.dot(img.affine, s0)  # adjust global bounding box offset to get global affine
-                voxdims = np.asanyarray(bbox.transform(result_affine).shape, dtype="int")
+                voxdims = np.asanyarray(np.ceil(
+                    bbox.transform(np.linalg.inv(result_affine)).shape
+                ), dtype="int")
                 result_arr = np.zeros(voxdims, dtype=img.dataobj.dtype)
                 result = nib.Nifti1Image(dataobj=result_arr, affine=result_affine)
 
-            arr = np.asanyarray(img.dataobj)
-            Xs, Ys, Zs = np.where(arr != 0)
-            Xt, Yt, Zt, _ = np.split(
-                (np.dot(
-                    np.linalg.inv(result_affine),
-                    np.dot(img.affine, np.c_[Xs, Ys, Zs, Zs * 0 + 1].T)
-                ) + .5).astype('int'),
-                4, axis=0
-            )
-            num_conflicts += np.count_nonzero(result_arr[Xt, Yt, Zt])
-            result_arr[Xt, Yt, Zt] = arr[Xs, Ys, Zs]
+            # resample to merge template and update it
+            resampled_img = resample_img_to_img(source_img=img, target_img=result)
+            arr = np.asanyarray(resampled_img.dataobj)
+            nonzero_voxels = arr != 0
+            num_conflicts += np.count_nonzero(result_arr[nonzero_voxels])
+            result_arr[nonzero_voxels] = arr[nonzero_voxels]
 
         if num_conflicts > 0:
             num_voxels = np.count_nonzero(result_arr)
-            logger.warning(f"Merging fragments required to overwrite {num_conflicts} conflicting voxels ({num_conflicts/num_voxels*100.:2.1f}%).")
+            logger.warning(
+                f"Merging fragments required to overwrite {num_conflicts} "
+                f"conflicting voxels ({num_conflicts / num_voxels * 100.:2.1f}%)."
+            )
 
         return result
 

siibra/volumes/sparsemap.py

@@ -458,7 +458,7 @@ class SparseMap(parcellationmap.Map):
         """
         Assign an image volume to this sparse map.
 
-        Parameters:
+        Parameters
         -----------
         queryvolume: Volume
             the volume to be compared with maps

siibra/volumes/volume.py

@@ -20,7 +20,7 @@ from .. import logger
 from ..retrieval import requests
 from ..core import space as _space, structure
 from ..locations import location, point, pointset, boundingbox
-from ..commons import resample_array_to_array, siibra_tqdm
+from ..commons import resample_img_to_img, siibra_tqdm
 from ..exceptions import NoMapAvailableError, SpaceWarpingFailedError
 
 from nibabel import Nifti1Image
@@ -52,7 +52,9 @@ class Volume(location.Location):
         "neuroglancer/precompmesh",
         "neuroglancer/precompmesh/surface",
         "gii-mesh",
-        "gii-label"
+        "gii-label",
+        "freesurfer-annot",
+        "zip/freesurfer-annot",
     ]
 
     SUPPORTED_FORMATS = IMAGE_FORMATS + MESH_FORMATS
@@ -86,7 +88,7 @@ class Volume(location.Location):
             assert srctype not in self._providers
             self._providers[srctype] = provider
         if len(self._providers) == 0:
-            logger.debug(f"No provider for volume {self}")
+            logger.debug(f"No provider for volume {name}")
 
     def __hash__(self):
         return super().__hash__()
@@ -141,7 +143,7 @@ class Volume(location.Location):
             If the volume provider does not have a bounding box calculator.
         """
         fmt = fetch_kwargs.get("format")
-        if fmt in self._providers:
+        if (fmt is not None) and (fmt not in self.formats):
             raise ValueError(
                 f"Requested format {fmt} is not available as provider of "
                 "this volume. See `volume.formats` for possible options."
@@ -157,7 +159,7 @@ class Volume(location.Location):
                     bbox.minpoint._space_cached = self.space
                     bbox.maxpoint._space_cached = self.space
             except NotImplementedError as e:
-                print(str(e))
+                logger.info(e)
                 continue
             return bbox
         raise RuntimeError(f"No bounding box specified by any volume provider of {str(self)}")
@@ -342,7 +344,7 @@ class Volume(location.Location):
             v1 = self.fetch(format=format, **fetch_kwargs)
             v2 = other.fetch(format=format, **fetch_kwargs)
             arr1 = np.asanyarray(v1.dataobj)
-            arr2 = resample_array_to_array(np.asanyarray(v2.dataobj), v2.affine, arr1, v1.affine)
+            arr2 = np.asanyarray(resample_img_to_img(v2, v1).dataobj)
             pointwise_min = np.minimum(arr1, arr2)
             if np.any(pointwise_min):
                 return from_array(
@@ -425,7 +427,7 @@ class Volume(location.Location):
             fwd_args = {k: v for k, v in kwargs.items() if k != "format"}
             for try_count in range(6):
                 try:
-                    if fmt == "gii-label":
+                    if fmt in ["gii-label", "freesurfer-annot", "zip/freesurfer-annot"]:
                         tpl = self.space.get_template(variant=kwargs.get('variant'))
                         mesh = tpl.fetch(**kwargs)
                         labels = self._providers[fmt].fetch(**fwd_args)
@@ -676,7 +678,6 @@ def merge(volumes: List[Volume], labels: List[int] = [], **fetch_kwargs) -> Volu
     assert all(v.space == space for v in volumes), "Cannot merge volumes from different spaces."
 
     template_img = space.get_template().fetch(**fetch_kwargs)
-    template_arr = np.asanyarray(template_img.dataobj)
     merged_array = np.zeros(template_img.shape, dtype='uint8')
 
     for i, vol in siibra_tqdm(
@@ -687,17 +688,14 @@ def merge(volumes: List[Volume], labels: List[int] = [], **fetch_kwargs) -> Volu
         disable=len(volumes) < 3
     ):
         img = vol.fetch(**fetch_kwargs)
-        arr_resampled = resample_array_to_array(
-            source_data=np.asanyarray(img.dataobj),
-            source_affine=img.affine,
-            target_data=template_arr,
-            target_affine=template_img.affine
+        resampled_arr = np.asanyarray(
+            resample_img_to_img(img, template_img).dataobj
         )
-        nonzero_voxels = arr_resampled > 0
+        nonzero_voxels = resampled_arr > 0
         if labels:
             merged_array[nonzero_voxels] = labels[i]
         else:
-            merged_array[nonzero_voxels] = arr_resampled[nonzero_voxels]
+            merged_array[nonzero_voxels] = resampled_arr[nonzero_voxels]
 
     return from_array(
         data=merged_array,

{siibra-1.0a8.dist-info → siibra-1.0a11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: siibra
-Version: 1.0a8
+Version: 1.0a11
 Summary: siibra - Software interfaces for interacting with brain atlases
 Home-page: https://github.com/FZJ-INM1-BDA/siibra-python
 Author: Big Data Analytics Group, Forschungszentrum Juelich, Institute of Neuroscience and Medicine (INM-1)

{siibra-1.0a8.dist-info → siibra-1.0a11.dist-info}/RECORD

@@ -1,16 +1,16 @@
-siibra/VERSION,sha256=lWuEdaPubq6hEIKFx_VdDGeYuyQVT53Swbs1o1Lo0OU,7
+siibra/VERSION,sha256=FkrBfNmMGsIgECPdtrQqgrSl5oiMXSJrUSM_-YKcX-E,7
 siibra/__init__.py,sha256=01VIBU4L5NLBTNFoAUskc7brJ-8TanNwl1Ejtl47YGI,4463
-siibra/commons.py,sha256=94cMkEbYfg-fLKGT6FByqhdhcBsVym-LoUC6F4_2XRY,27532
+siibra/commons.py,sha256=ke6CI3vzMHIveJE8Xw9xZ126JrMFqApUsA1hiOyP6ls,28813
 siibra/exceptions.py,sha256=bs79_vEK9Dz4TntJnD66L_bJ5Tt4Z0mO9GXQ4f9kNQE,1109
 siibra/configuration/__init__.py,sha256=-_Kuf0TfMEdFXiSCTAdcHUL_krA8-cxhJypSNNay53Q,752
 siibra/configuration/configuration.py,sha256=p2R0dxD8HdvrwHokXuTCrVgz9DvXmEmHkxRL_oT0VRI,7263
-siibra/configuration/factory.py,sha256=nTvV31QLlbnUq_j1WGEd0blGw_fBubYx1Sy9XFfQbjE,21109
+siibra/configuration/factory.py,sha256=4IGayJJ47PXa9jdwnmcrPLeYa0Pmu1EJehG4LR-smbw,21110
 siibra/core/__init__.py,sha256=YQkeqGqpOT3aH-PPHeGb1kxSyMbgR3ZHqDCy2I0Zlsk,735
 siibra/core/assignment.py,sha256=pWkivLA54NrX3j21E_YxSX9_S70MrGuGq_6aQQ5IBB4,3819
-siibra/core/atlas.py,sha256=Fj5o4ehlh4BpCdu-LuT9im21_NioWMxhFbIApqF9Mxg,7865
+siibra/core/atlas.py,sha256=XZ0vy6_l-kuiNF6KYs1PpTk2XwBK-aMY6cUKUnLYb3A,8299
 siibra/core/concept.py,sha256=zL220pIYmqWhEZNMo01p2o0IC37rjApdNd1_dPmbNvU,10496
 siibra/core/parcellation.py,sha256=iIESwMVg-YQLkCn7KSj8LZl1QDttMxJOVGoRv7DL2kU,13873
-siibra/core/region.py,sha256=8n5EZQnQcDb60yygH3nR9-VLFRj5mEDkkhRCB-20t_s,38663
+siibra/core/region.py,sha256=2tDlrjoVKTz2dO4Y3Q2GAVPIWbZuDnGc04iEOPLPveM,44049
 siibra/core/space.py,sha256=TvOvcBKextuRrptdFKU-je6w5g5lqK0I_Wga73jd0zk,4517
 siibra/core/structure.py,sha256=cZFR_eyXt6j2KT6ohiOQFnjmntFVcvA4k2FpSinPzWI,4498
 siibra/experimental/__init__.py,sha256=s4bEYpMO4Ox-Xlx3FdnRUNKYs0mTHz5Hu4VnfNXpgxU,791
@@ -21,63 +21,64 @@ siibra/experimental/plane3d.py,sha256=Z1MnK3qjGvYLGgNcAimgCejBhAOzcwfF8cYyajTLrA
 siibra/explorer/__init__.py,sha256=9TYF4i5o3guwqDtsQ7mV6MLVmKQIFG0AwxN8PA_6ctw,781
 siibra/explorer/url.py,sha256=kxfrfz8v6gl_Z2Vu4jJkb54WYk8reFJxf3TXhJGu2VQ,6421
 siibra/explorer/util.py,sha256=8Ap0tnVFk1LOzD70o-EUbHk6HPLAG4SLaDrvrEzaJGk,2083
-siibra/features/__init__.py,sha256=_0iV-NiIqci9PkkYIzdm8Fl474HXYtzFw14VC9xrdOE,3428
+siibra/features/__init__.py,sha256=Jd19RXFBuVemhF6AtrhOG4luocYGauA0FjnaEZdyaa8,3970
 siibra/features/anchor.py,sha256=cp5cu-tJceenbJESXLe3DXhmjtdhdyTN0KYOIXDkhmU,9068
-siibra/features/feature.py,sha256=c9jKLfgp0Eza1z53MiOcI95YMZfIbC5t7wM9tYctVDc,32572
+siibra/features/feature.py,sha256=MXhUZtf_7qwqQuVnmNtqTMfLMvGyVaN8O0ilFqIwv9A,34359
 siibra/features/connectivity/__init__.py,sha256=XU6w7kX6lN_fZLt0TFGqg39Z9FCfbcotSR79p-JhLV4,1161
-siibra/features/connectivity/functional_connectivity.py,sha256=9xHu_GaODGP6Q0--hTf_tMjLtg1IKWI4qw78sZ9GQ5M,2120
-siibra/features/connectivity/regional_connectivity.py,sha256=zNohbWDBq7fWz7EDIZjFEDNwMgKnvDfkq9lLUKNfSDw,16736
+siibra/features/connectivity/functional_connectivity.py,sha256=USnlse_qmThBxqINnv9EmecQewxuOvK3Mzy3DqbQBzc,2122
+siibra/features/connectivity/regional_connectivity.py,sha256=uweR77YFQ27B3jzbHu854NRsqUj8aA9ISTz0r7lMe9U,18211
 siibra/features/connectivity/streamline_counts.py,sha256=ngl7xCiCUOyflyBvjZYa3ShOmtf21E5e0A_BeWfFtSQ,1064
 siibra/features/connectivity/streamline_lengths.py,sha256=0a09Dag-eRvs1KgHSU47I3xQwbgHICsDozhZyuNzQME,1067
 siibra/features/connectivity/tracing_connectivity.py,sha256=pyTMTLvkJL3ftk56s0AbT8dHexV4EyuTJ2yX27kLGfc,1083
 siibra/features/dataset/__init__.py,sha256=5h_wstfa3h35emL1qoKOtcFOiIjKZX9oIy-GwsChEyc,748
 siibra/features/dataset/ebrains.py,sha256=0cul8rtp6n1lCxTOfLL2AYCWx36q2ILezTXk2i44few,2544
 siibra/features/image/__init__.py,sha256=UIECVLwKYKeuCPNa4WcjcLDuNr_3JxCyiOQSjBRf36U,1013
-siibra/features/image/image.py,sha256=BOX7lx5w8sAgLVLp_pu1E8Kk2zbtEs420rCOL_BWvu0,3342
+siibra/features/image/image.py,sha256=XJczatDzEvEbihq5I6hq5IuifN9avCbieRoVxdoZLpc,3384
 siibra/features/image/sections.py,sha256=d4TQSs6nIKQ5vgi89htERfWOMgnvOA9k4LhaXBMWNbE,961
 siibra/features/image/volume_of_interest.py,sha256=DIv9GNOptfungLddA_CfrrCfY8p36rbWCT9xkE6K66w,2654
 siibra/features/tabular/__init__.py,sha256=3DBwa8JtGd-npeOyyw6kJzcveKXadbqSATyJtTnY3-w,1176
-siibra/features/tabular/bigbrain_intensity_profile.py,sha256=Yt3wa8WWjA0F0uzmLwbamIthEmkEQovcRrof94Hr3dQ,2707
-siibra/features/tabular/cell_density_profile.py,sha256=YFC64ghEf5AfnyAALMdFE4ZAVbCsTOCFek2gNP6F83k,9245
-siibra/features/tabular/cortical_profile.py,sha256=euyAxi5C2Ths0fR93oM5B9oD9ej73dslVabDr4XH2Qo,9632
-siibra/features/tabular/gene_expression.py,sha256=r6XsmejxYVd0-pfZxHwu5QsA4ipZiEK_QE47J7agrk0,5035
-siibra/features/tabular/layerwise_bigbrain_intensities.py,sha256=051Jd78h-Ndva3vEW-Ch2sYnG6m1H2sRT6xDVX_tBWk,2118
-siibra/features/tabular/layerwise_cell_density.py,sha256=CJMcUeN_aawfCzZTLq4xKq-Kas5sHFNVNVL6bqhCOEc,4167
-siibra/features/tabular/receptor_density_fingerprint.py,sha256=oQAK2nk_zcxyySHdimdmNXjkgEwnMDszPqZlS5bcJA4,7186
-siibra/features/tabular/receptor_density_profile.py,sha256=bBAiLdbF2Lgnc8_33R2XoFQmyie96j5dQsBIkzXsRw0,3702
-siibra/features/tabular/regional_timeseries_activity.py,sha256=A2GiDVojuOaH73f4ql8BcHWW7uS2WqfQjL6svSydJEI,8251
-siibra/features/tabular/tabular.py,sha256=rZHCA71x6Trx2jOj1pBWZblmCc3jI3PzhMS-nxzMS-E,5210
+siibra/features/tabular/bigbrain_intensity_profile.py,sha256=M2b5Qg75hrsy6CxnSRvdMq-wGjUOATMLt8b4OxfL1us,2706
+siibra/features/tabular/cell_density_profile.py,sha256=kzjsOt_dM3dpvaBQlKZKlfvFjYpvwOpsF0WzNEERfos,9289
+siibra/features/tabular/cortical_profile.py,sha256=Mvp_vobov8z7k0tgqNMRYPdaX3o2cGFvvkC58KQ9BKE,12469
+siibra/features/tabular/gene_expression.py,sha256=3NxSdPNFLKvug69hgduNnds4JQ4wnTeVMFkJq6fCBiY,9803
+siibra/features/tabular/layerwise_bigbrain_intensities.py,sha256=saUb1vzXX4zbmrZwrjpOx0VlPFLEJ9NXZjtouRz33oc,2117
+siibra/features/tabular/layerwise_cell_density.py,sha256=eJxVq794rI7_Tb2K1f8x5j8jXrh_E7XzoXlQA1UVdTw,4209
+siibra/features/tabular/receptor_density_fingerprint.py,sha256=iJMBoILm1vVq2jFP8RCvKyAXHtv00iVbgbuo-2RT3to,7228
+siibra/features/tabular/receptor_density_profile.py,sha256=l8i6WICH1o_J_8wDjnqXdadQIR6Mdoz9VCmaYzuUd_4,3655
+siibra/features/tabular/regional_timeseries_activity.py,sha256=HhdavuEFWWWTmBFNg50HdLipGsJBmqAY7mTVGo7oA0U,9949
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