3697 add spatial resample

.github/workflows/integration.yml

@@ -3,6 +3,9 @@ name: integration
 on:
   repository_dispatch:
     type: [integration-test-command]
+  push:
+    branches:
+      - add-spatial-resample
 
 jobs:
   integration-py3:
@@ -32,7 +35,7 @@ jobs:
     - name: Install the dependencies
       run: |
         which python
-        python -m pip install --upgrade pip wheel
+        python -m pip install --upgrade pip==21.3.1 wheel  # workaround monai##3752
         python -m pip uninstall -y torch torchvision
         python -m pip install torch==1.10.1+cu111 torchvision==0.11.2+cu111 -f https://download.pytorch.org/whl/torch_stable.html
         python -m pip install -r requirements-dev.txt

docs/source/transforms.rst

@@ -557,6 +557,12 @@ Post-processing
 Spatial
 ^^^^^^^
 
+`SpatialResample`
+"""""""""""""""""
+.. autoclass:: SpatialResample
+    :members:
+    :special-members: __call__
+
 `Spacing`
 """""""""
 .. image:: https://github.com/Project-MONAI/DocImages/raw/main/transforms/Spacing.png
@@ -1398,6 +1404,12 @@ Post-processing (Dict)
 Spatial (Dict)
 ^^^^^^^^^^^^^^
 
+`SpatialResampled`
+""""""""""""""""""
+.. autoclass:: SpatialResampled
+    :members:
+    :special-members: __call__
+
 `Spacingd`
 """"""""""
 .. image:: https://github.com/Project-MONAI/DocImages/raw/main/transforms/Spacingd.png

monai/apps/deepgrow/transforms.py

@@ -374,7 +374,7 @@ class SpatialCropForegroundd(MapTransform):
             the meta data is a dictionary object which contains: filename, original_shape, etc.
             it can be a sequence of string, map to the `keys`.
             if None, will try to construct meta_keys by `key_{meta_key_postfix}`.
-        meta_key_postfix: if meta_keys is None, use `{key}_{meta_key_postfix}` to to fetch/store the meta data according
+        meta_key_postfix: if meta_keys is None, use `{key}_{meta_key_postfix}` to fetch/store the meta data according
             to the key data, default is `meta_dict`, the meta data is a dictionary object.
             For example, to handle key `image`,  read/write affine matrices from the
             metadata `image_meta_dict` dictionary's `affine` field.
@@ -474,7 +474,7 @@ class AddGuidanceFromPointsd(Transform):
             for example, for data with key `image`, the metadata by default is in `image_meta_dict`.
             the meta data is a dictionary object which contains: filename, original_shape, etc.
             if None, will try to construct meta_keys by `{ref_image}_{meta_key_postfix}`.
-        meta_key_postfix: if meta_key is None, use `{ref_image}_{meta_key_postfix}` to to fetch the meta data according
+        meta_key_postfix: if meta_key is None, use `{ref_image}_{meta_key_postfix}` to fetch the meta data according
             to the key data, default is `meta_dict`, the meta data is a dictionary object.
             For example, to handle key `image`,  read/write affine matrices from the
             metadata `image_meta_dict` dictionary's `affine` field.
@@ -589,7 +589,7 @@ class SpatialCropGuidanced(MapTransform):
             the meta data is a dictionary object which contains: filename, original_shape, etc.
             it can be a sequence of string, map to the `keys`.
             if None, will try to construct meta_keys by `key_{meta_key_postfix}`.
-        meta_key_postfix: if meta_keys is None, use `key_{postfix}` to to fetch the meta data according
+        meta_key_postfix: if meta_keys is None, use `key_{postfix}` to fetch the meta data according
             to the key data, default is `meta_dict`, the meta data is a dictionary object.
             For example, to handle key `image`,  read/write affine matrices from the
             metadata `image_meta_dict` dictionary's `affine` field.
@@ -787,7 +787,7 @@ class RestoreLabeld(MapTransform):
             the meta data is a dictionary object which contains: filename, original_shape, etc.
             it can be a sequence of string, map to the `keys`.
             if None, will try to construct meta_keys by `key_{meta_key_postfix}`.
-        meta_key_postfix: if meta_key is None, use `key_{meta_key_postfix} to to fetch the meta data according
+        meta_key_postfix: if meta_key is None, use `key_{meta_key_postfix} to fetch the meta data according
             to the key data, default is `meta_dict`, the meta data is a dictionary object.
             For example, to handle key `image`,  read/write affine matrices from the
             metadata `image_meta_dict` dictionary's `affine` field.
@@ -897,7 +897,7 @@ class Fetch2DSliced(MapTransform):
             the meta data is a dictionary object which contains: filename, original_shape, etc.
             it can be a sequence of string, map to the `keys`.
             if None, will try to construct meta_keys by `key_{meta_key_postfix}`.
-        meta_key_postfix: use `key_{meta_key_postfix}` to to fetch the meta data according to the key data,
+        meta_key_postfix: use `key_{meta_key_postfix}` to fetch the meta data according to the key data,
             default is `meta_dict`, the meta data is a dictionary object.
             For example, to handle key `image`,  read/write affine matrices from the
             metadata `image_meta_dict` dictionary's `affine` field.

monai/csrc/ext.cpp

@@ -31,6 +31,7 @@ PYBIND11_MODULE(TORCH_EXTENSION_NAME, m) {
   py::enum_<monai::BoundType>(m, "BoundType")
       .value("replicate", monai::BoundType::Replicate, "a a a | a b c d | d d d")
       .value("nearest", monai::BoundType::Replicate, "a a a | a b c d | d d d")
+      .value("border", monai::BoundType::Replicate, "a a a | a b c d | d d d")
       .value("dct1", monai::BoundType::DCT1, "d c b | a b c d | c b a")
       .value("mirror", monai::BoundType::DCT1, "d c b | a b c d | c b a")
       .value("dct2", monai::BoundType::DCT2, "c b a | a b c d | d c b")
@@ -43,6 +44,7 @@ PYBIND11_MODULE(TORCH_EXTENSION_NAME, m) {
       .value("wrap", monai::BoundType::DFT, "b c d | a b c d | a b c")
       //   .value("sliding", monai::BoundType::Sliding)
       .value("zero", monai::BoundType::Zero, "0 0 0 | a b c d | 0 0 0")
+      .value("zeros", monai::BoundType::Zero, "0 0 0 | a b c d | 0 0 0")
       .export_values();
 
   // resample interpolation mode

monai/csrc/resample/pushpull_cpu.cpp

@@ -1527,10 +1527,10 @@ MONAI_NAMESPACE_DEVICE { // cpu
     iy0 = bound::index(bound1, iy0, src_Y);
     iz0 = bound::index(bound2, iz0, src_Z);
 
-    // Offsets into source volume
     offset_t o000, o100, o010, o001, o110, o011, o101, o111;
 
     if (do_pull || do_grad || do_sgrad) {
+      // Offsets into source volume
       o000 = ix0 * src_sX + iy0 * src_sY + iz0 * src_sZ;
       o100 = ix1 * src_sX + iy0 * src_sY + iz0 * src_sZ;
       o010 = ix0 * src_sX + iy1 * src_sY + iz0 * src_sZ;
@@ -1539,18 +1539,20 @@ MONAI_NAMESPACE_DEVICE { // cpu
       o011 = ix0 * src_sX + iy1 * src_sY + iz1 * src_sZ;
       o101 = ix1 * src_sX + iy0 * src_sY + iz1 * src_sZ;
       o111 = ix1 * src_sX + iy1 * src_sY + iz1 * src_sZ;
+    } else {
+      // Offsets into 'push' volume
+      o000 = ix0 * out_sX + iy0 * out_sY + iz0 * out_sZ;
+      o100 = ix1 * out_sX + iy0 * out_sY + iz0 * out_sZ;
+      o010 = ix0 * out_sX + iy1 * out_sY + iz0 * out_sZ;
+      o001 = ix0 * out_sX + iy0 * out_sY + iz1 * out_sZ;
+      o110 = ix1 * out_sX + iy1 * out_sY + iz0 * out_sZ;
+      o011 = ix0 * out_sX + iy1 * out_sY + iz1 * out_sZ;
+      o101 = ix1 * out_sX + iy0 * out_sY + iz1 * out_sZ;
+      o111 = ix1 * out_sX + iy1 * out_sY + iz1 * out_sZ;
     }
 
     // ~~~~~~~~~~~~~~~~~~~~~~~~~~ Grid gradient ~~~~~~~~~~~~~~~~~~~~~~~~~~
     if (do_grad) {
-      o000 = ix0 * src_sX + iy0 * src_sY + iz0 * src_sZ;
-      o100 = ix1 * src_sX + iy0 * src_sY + iz0 * src_sZ;
-      o010 = ix0 * src_sX + iy1 * src_sY + iz0 * src_sZ;
-      o001 = ix0 * src_sX + iy0 * src_sY + iz1 * src_sZ;
-      o110 = ix1 * src_sX + iy1 * src_sY + iz0 * src_sZ;
-      o011 = ix0 * src_sX + iy1 * src_sY + iz1 * src_sZ;
-      o101 = ix1 * src_sX + iy0 * src_sY + iz1 * src_sZ;
-      o111 = ix1 * src_sX + iy1 * src_sY + iz1 * src_sZ;
       scalar_t gx = static_cast<scalar_t>(0);
       scalar_t gy = static_cast<scalar_t>(0);
       scalar_t gz = static_cast<scalar_t>(0);
@@ -1659,14 +1661,6 @@ MONAI_NAMESPACE_DEVICE { // cpu
     }
     // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Pull ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     if (do_pull) {
-      o000 = ix0 * src_sX + iy0 * src_sY + iz0 * src_sZ;
-      o100 = ix1 * src_sX + iy0 * src_sY + iz0 * src_sZ;
-      o010 = ix0 * src_sX + iy1 * src_sY + iz0 * src_sZ;
-      o001 = ix0 * src_sX + iy0 * src_sY + iz1 * src_sZ;
-      o110 = ix1 * src_sX + iy1 * src_sY + iz0 * src_sZ;
-      o011 = ix0 * src_sX + iy1 * src_sY + iz1 * src_sZ;
-      o101 = ix1 * src_sX + iy0 * src_sY + iz1 * src_sZ;
-      o111 = ix1 * src_sX + iy1 * src_sY + iz1 * src_sZ;
       scalar_t* out_ptr_NCXYZ = out_ptr + n * out_sN + w * out_sX + h * out_sY + d * out_sZ;
       scalar_t* src_ptr_NC = src_ptr + n * src_sN;
       for (offset_t c = 0; c < C; ++c, out_ptr_NCXYZ += out_sC, src_ptr_NC += src_sC) {
@@ -1678,14 +1672,6 @@ MONAI_NAMESPACE_DEVICE { // cpu
     }
     // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SGrad ~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~
     else if (do_sgrad) {
-      o000 = ix0 * src_sX + iy0 * src_sY + iz0 * src_sZ;
-      o100 = ix1 * src_sX + iy0 * src_sY + iz0 * src_sZ;
-      o010 = ix0 * src_sX + iy1 * src_sY + iz0 * src_sZ;
-      o001 = ix0 * src_sX + iy0 * src_sY + iz1 * src_sZ;
-      o110 = ix1 * src_sX + iy1 * src_sY + iz0 * src_sZ;
-      o011 = ix0 * src_sX + iy1 * src_sY + iz1 * src_sZ;
-      o101 = ix1 * src_sX + iy0 * src_sY + iz1 * src_sZ;
-      o111 = ix1 * src_sX + iy1 * src_sY + iz1 * src_sZ;
       scalar_t* out_ptr_NCXYZ = out_ptr + n * out_sN + w * out_sX + h * out_sY + d * out_sZ;
       scalar_t* src_ptr_NC = src_ptr + n * src_sN;
 
@@ -1758,16 +1744,6 @@ MONAI_NAMESPACE_DEVICE { // cpu
     }
     // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Push ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     else if (do_count) {
-      // Offsets into 'push' volume
-      o000 = ix0 * out_sX + iy0 * out_sY + iz0 * out_sZ;
-      o100 = ix1 * out_sX + iy0 * out_sY + iz0 * out_sZ;
-      o010 = ix0 * out_sX + iy1 * out_sY + iz0 * out_sZ;
-      o001 = ix0 * out_sX + iy0 * out_sY + iz1 * out_sZ;
-      o110 = ix1 * out_sX + iy1 * out_sY + iz0 * out_sZ;
-      o011 = ix0 * out_sX + iy1 * out_sY + iz1 * out_sZ;
-      o101 = ix1 * out_sX + iy0 * out_sY + iz1 * out_sZ;
-      o111 = ix1 * out_sX + iy1 * out_sY + iz1 * out_sZ;
-
       scalar_t* out_ptr_N = out_ptr + n * out_sN;
       bound::add(out_ptr_N, o000, w000, s000);
       bound::add(out_ptr_N, o100, w100, s100);
@@ -1822,21 +1798,23 @@ MONAI_NAMESPACE_DEVICE { // cpu
     ix0 = bound::index(bound0, ix0, src_X);
     iy0 = bound::index(bound1, iy0, src_Y);
 
-    // Offsets into source volume
     offset_t o00, o10, o01, o11;
     if (do_pull || do_grad || do_sgrad) {
+      // Offsets into source volume
       o00 = ix0 * src_sX + iy0 * src_sY;
       o10 = ix1 * src_sX + iy0 * src_sY;
       o01 = ix0 * src_sX + iy1 * src_sY;
       o11 = ix1 * src_sX + iy1 * src_sY;
+    } else {
+      // Offsets into 'push' volume
+      o00 = ix0 * out_sX + iy0 * out_sY;
+      o10 = ix1 * out_sX + iy0 * out_sY;
+      o01 = ix0 * out_sX + iy1 * out_sY;
+      o11 = ix1 * out_sX + iy1 * out_sY;
     }
 
     // ~~~~~~~~~~~~~~~~~~~~~~~~~~ Grid gradient ~~~~~~~~~~~~~~~~~~~~~~~~~~
     if (do_grad) {
-      o00 = ix0 * src_sX + iy0 * src_sY;
-      o10 = ix1 * src_sX + iy0 * src_sY;
-      o01 = ix0 * src_sX + iy1 * src_sY;
-      o11 = ix1 * src_sX + iy1 * src_sY;
       scalar_t gx = static_cast<scalar_t>(0);
       scalar_t gy = static_cast<scalar_t>(0);
       scalar_t* trgt_ptr_NCXY = trgt_ptr + n * trgt_sN + w * trgt_sX + h * trgt_sY;
@@ -1895,10 +1873,6 @@ MONAI_NAMESPACE_DEVICE { // cpu
     }
     // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Pull ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     if (do_pull) {
-      o00 = ix0 * src_sX + iy0 * src_sY;
-      o10 = ix1 * src_sX + iy0 * src_sY;
-      o01 = ix0 * src_sX + iy1 * src_sY;
-      o11 = ix1 * src_sX + iy1 * src_sY;
       scalar_t* out_ptr_NCXY = out_ptr + n * out_sN + w * out_sX + h * out_sY;
       scalar_t* src_ptr_NC = src_ptr + n * src_sN;
       for (offset_t c = 0; c < C; ++c, out_ptr_NCXY += out_sC, src_ptr_NC += src_sC) {
@@ -1908,10 +1882,6 @@ MONAI_NAMESPACE_DEVICE { // cpu
     }
     // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SGrad ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     else if (do_sgrad) {
-      o00 = ix0 * src_sX + iy0 * src_sY;
-      o10 = ix1 * src_sX + iy0 * src_sY;
-      o01 = ix0 * src_sX + iy1 * src_sY;
-      o11 = ix1 * src_sX + iy1 * src_sY;
       scalar_t* out_ptr_NCXY = out_ptr + n * out_sN + w * out_sX + h * out_sY;
       scalar_t* src_ptr_NC = src_ptr + n * src_sN;
 
@@ -1926,11 +1896,6 @@ MONAI_NAMESPACE_DEVICE { // cpu
     }
     // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Push ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     else if (do_push) {
-      // Offsets into 'push' volume
-      o00 = ix0 * out_sX + iy0 * out_sY;
-      o10 = ix1 * out_sX + iy0 * out_sY;
-      o01 = ix0 * out_sX + iy1 * out_sY;
-      o11 = ix1 * out_sX + iy1 * out_sY;
       scalar_t* trgt_ptr_NCXY = trgt_ptr + n * trgt_sN + w * trgt_sX + h * trgt_sY;
       scalar_t* out_ptr_NC = out_ptr + n * out_sN;
       if (trgt_K == 0) {
@@ -1960,12 +1925,6 @@ MONAI_NAMESPACE_DEVICE { // cpu
     }
     // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Push ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     else if (do_count) {
-      // Offsets into 'push' volume
-      o00 = ix0 * out_sX + iy0 * out_sY;
-      o10 = ix1 * out_sX + iy0 * out_sY;
-      o01 = ix0 * out_sX + iy1 * out_sY;
-      o11 = ix1 * out_sX + iy1 * out_sY;
-
       scalar_t* out_ptr_N = out_ptr + n * out_sN;
       bound::add(out_ptr_N, o00, w00, s00);
       bound::add(out_ptr_N, o10, w10, s10);
@@ -1996,20 +1955,21 @@ MONAI_NAMESPACE_DEVICE { // cpu
     ix1 = bound::index(bound0, ix0 + 1, src_X);
     ix0 = bound::index(bound0, ix0, src_X);
 
-    // Offsets into source volume
     offset_t o0, o1;
     if (do_pull || do_grad || do_sgrad) {
+      // Offsets into source volume
       o0 = ix0 * src_sX;
       o1 = ix1 * src_sX;
+    } else {
+      // Offsets into 'push' volume
+      o0 = ix0 * out_sX;
+      o1 = ix1 * out_sX;
     }
 
     // ~~~~~~~~~~~~~~~~~~~~~~~~~~ Grid gradient ~~~~~~~~~~~~~~~~~~~~~~~~~~
     if (do_grad) {
       if (trgt_K == 0) {
         // backward w.r.t. push/pull
-
-        o0 = ix0 * src_sX;
-        o1 = ix1 * src_sX;
         scalar_t gx = static_cast<scalar_t>(0);
         scalar_t* trgt_ptr_NCX = trgt_ptr + n * trgt_sN + w * trgt_sX;
         scalar_t* src_ptr_NC = src_ptr + n * src_sN;
@@ -2037,8 +1997,6 @@ MONAI_NAMESPACE_DEVICE { // cpu
     }
     // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Pull ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     if (do_pull) {
-      o0 = ix0 * src_sX;
-      o1 = ix1 * src_sX;
       scalar_t* out_ptr_NCX = out_ptr + n * out_sN + w * out_sX;
       scalar_t* src_ptr_NC = src_ptr + n * src_sN;
       for (offset_t c = 0; c < C; ++c, out_ptr_NCX += out_sC, src_ptr_NC += src_sC) {
@@ -2047,8 +2005,6 @@ MONAI_NAMESPACE_DEVICE { // cpu
     }
     // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SGrad ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     else if (do_sgrad) {
-      o0 = ix0 * src_sX;
-      o1 = ix1 * src_sX;
       scalar_t* out_ptr_NCX = out_ptr + n * out_sN + w * out_sX;
       scalar_t* src_ptr_NC = src_ptr + n * src_sN;
 
@@ -2058,9 +2014,6 @@ MONAI_NAMESPACE_DEVICE { // cpu
     }
     // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Push ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     else if (do_push) {
-      // Offsets into 'push' volume
-      o0 = ix0 * out_sX;
-      o1 = ix1 * out_sX;
       scalar_t* trgt_ptr_NCX = trgt_ptr + n * trgt_sN + w * trgt_sX;
       scalar_t* out_ptr_NC = out_ptr + n * out_sN;
       if (trgt_K == 0) {
@@ -2081,10 +2034,6 @@ MONAI_NAMESPACE_DEVICE { // cpu
     }
     // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Push ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     else if (do_count) {
-      // Offsets into 'push' volume
-      o0 = ix0 * out_sX;
-      o1 = ix1 * out_sX;
-
       scalar_t* out_ptr_N = out_ptr + n * out_sN;
       bound::add(out_ptr_N, o0, w0, s0);
       bound::add(out_ptr_N, o1, w1, s1);