tinybrain 1.7.0__tar.gz → 1.8.0__tar.gz

{tinybrain-1.7.0 → tinybrain-1.8.0}/.github/workflows/build_wheel.yml

@@ -6,7 +6,7 @@ on:
     tags:
       - '*'
 env:
-  CIBW_SKIP: pp* *-musllinux*
+  CIBW_SKIP: pp* cp315t*
 
 jobs:
   build_wheels:
@@ -14,21 +14,17 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-2019, macos-latest]
+        os: [ubuntu-latest, macos-latest, windows-latest]
         arch: [auto]
         include:
-          - os: ubuntu-latest
+          - os: ubuntu-24.04-arm
             arch: aarch64
 
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up QEMU
-        if:  ${{ matrix.arch == 'aarch64' }}
-        uses: docker/setup-qemu-action@v1
-
       - name: Build wheels
-        uses: joerick/cibuildwheel@v2.22.0
+        uses: joerick/cibuildwheel@v4.2.0
         # to supply options, put them in 'env', like:
         env:
           CIBW_BEFORE_BUILD: pip install numpy pybind11 setuptools wheel pkginfo twine

{tinybrain-1.7.0 → tinybrain-1.8.0}/.github/workflows/run_tests.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14", "3.15"]
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}
@@ -23,7 +23,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v7
 
       - name: Install dependencies
         run: |

{tinybrain-1.7.0 → tinybrain-1.8.0}/ChangeLog

@@ -1,6 +1,19 @@
 CHANGES
 =======
 
+1.8.0
+-----
+
+* ci: skip building cp315t
+* release(1.8.0): support boolean images, faster 2x2x2 mode downsampling
+* ci: update build
+* fix: error and missing optimization
+* test: add compliance test for end of 2x2x2
+* docs: update performance numbers for 2x2x2 mode
+* perf: faster 2x2x2 mode downsampling
+* feat: support mode pooling for boolean images
+* test: update benchmark with Macbook Pro M3 + add pillow, opencv
+
 1.7.0
 -----
 

{tinybrain-1.7.0 → tinybrain-1.8.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: tinybrain
-Version: 1.7.0
+Version: 1.8.0
 Summary: Image pyramid generation specialized for connectomics data types and procedures.
 Home-page: https://github.com/seung-lab/tinybrain/
 Author: William Silversmith

{tinybrain-1.7.0 → tinybrain-1.8.0}/automated_test.py

@@ -700,6 +700,21 @@ def test_sparse_2x2x2_mode_downsampling(dtype):
   assert res[0][0][0] == 0
   assert res.shape == (1,1,1)
 
+  test7 = np.array([
+    [
+      [1,2],
+      [3,4],
+    ],
+    [
+      [5,6],
+      [7,8],
+    ],
+  ], dtype=dtype, order='F')
+
+  res = tinybrain.accelerated.mode_pooling_2x2x2(test7, sparse=True)[0]
+  assert res[0][0][0] == 1
+  assert res.shape == (1,1,1)
+
   # test7 = np.array([
   #   [
   #     [1,0,1],

{tinybrain-1.7.0 → tinybrain-1.8.0}/perf.py

@@ -27,6 +27,26 @@
 # 2x2x2 1 mip sparse: 0.656s, 2041.96 MVx/sec, N=10
 # 2x2x2 2 mip sparse: 0.762s, 1758.42 MVx/sec, N=10
 
+# Results on a 2023 Macbook Pro M3
+# AVG POOLING ((2048, 2048, 64), uint8)
+# 2x2 1 mip: 0.084s, 31954.51 MVx/sec, N=10
+# 2x2 2 mip: 0.223s, 11995.13 MVx/sec, N=10
+# 2x2x2 1 mip: 0.042s, 63958.66 MVx/sec, N=10
+# 2x2x2 2 mip: 0.218s, 12303.19 MVx/sec, N=10
+# 2x2x2 1 mip sparse: 0.581s, 4612.79 MVx/sec, N=10
+# 2x2x2 2 mip sparse: 0.686s, 3908.00 MVx/sec, N=10
+# 2x2 1 mip pillow: 10.526s, 254.61 MVx/sec, N=10
+# 2x2 1 mip opencv: 5.352s, 500.79 MVx/sec, N=10
+# MODE POOLING ((2048, 2048, 64), uint64)
+# 2x2 1 mip: 1.030s, 2602.65 MVx/sec, N=10
+# 2x2 2 mip: 1.181s, 2269.54 MVx/sec, N=10
+# 2x2 1 mip sparse: 14.294s, 187.49 MVx/sec, N=10
+# 2x2 2 mip sparse: 25.615s, 104.63 MVx/sec, N=10
+# 2x2x2 1 mip: 3.171s, 845.10 MVx/sec, N=10
+# 2x2x2 2 mip: 3.479s, 770.30 MVx/sec, N=10
+# 2x2x2 1 mip sparse: 3.461s, 774.31 MVx/sec, N=10
+# 2x2x2 2 mip sparse: 3.916s, 684.42 MVx/sec, N=10
+
 import numpy as np
 import tinybrain
 import time
@@ -80,6 +100,33 @@ def benchmark_avg_pooling():
 	end = time.time()
 	result("2x2x2 2 mip sparse", end - start, data, N)
 
+	try:
+		from PIL import Image
+		s = time.time()
+		out = np.zeros([1024,1024,64], dtype=np.uint8, order="F")
+		for _ in range(N):
+			for z in range(data.shape[2]):
+			  pilimg = Image.fromarray(data[:,:,z])
+			  out[:,:,z] = pilimg.resize( (1024, 1024) )
+		end = time.time()
+		result("2x2 1 mip pillow", end - start, data, N)
+		del out
+	except ImportError:
+		print("Pillow not installed.")
+
+	try:
+		import cv2
+		start = time.time()
+		out = np.zeros(shape=(1024,1024,64))
+		for _ in range(N):
+			for z in range(data.shape[2]):
+			  out[:,:,z] = cv2.resize(data[:,:,z], dsize=(1024, 1024) )
+		end = time.time()
+		result("2x2 1 mip opencv", end - start, data, N)
+		del out
+	except ImportError:
+		print("opencv not installed.")
+
 def benchmark_mode_pooling():
 	data = np.random.randint(1000,1255, size=(2048,2048,64), dtype=np.uint64)
 	data = np.asfortranarray(data)

{tinybrain-1.7.0 → tinybrain-1.8.0}/tinybrain/__init__.py

@@ -7,4 +7,4 @@ from .downsample import (
   DimensionError
 )
 
-__version__ = '1.4.1'
+__version__ = '1.8.0'

{tinybrain-1.7.0 → tinybrain-1.8.0}/tinybrain/accelerated.hpp

@@ -1114,19 +1114,26 @@ inline void _mode_pooling_2x2x2(
               continue;
             }
 
-            max_ct = 0;
-            max_val = 0;
-            for (short int t = 0; t < 8; t++) {
+            if (sparse && vals[0] == 0) {
+              max_ct = 0;
+              max_val = 0;
+            }
+            else {
+              max_ct = 1;
+              max_val = vals[0];
+            }
+
+            // no need to evaluate t=0, as if max_ct
+            // is 1 at the last entry, it can't go higher than
+            // 1, so we'll just take the last entry as good
+            for (short int t = 7; t >= 1; t--) {
               cur_val = vals[t];
               if (sparse && cur_val == 0) {
                 continue;
               }
 
               cur_ct = 1;
-              for (short int p = 0; p < t; p++) {
-                cur_ct += (cur_val == vals[p]);
-              }
-              for (short int p = t + 1; p < 8; p++) {
+              for (short int p = t-1; p >= 0; p--) {
                 cur_ct += (cur_val == vals[p]);
               }
 

{tinybrain-1.7.0 → tinybrain-1.8.0}/tinybrain/downsample.py

@@ -230,6 +230,11 @@ def downsample_segmentation(img, factor, sparse=False, num_mips=1):
   if np.all(np.array(factor, int) == 1):
       return [ img ] * num_mips
 
+  binary_image = isinstance(img, (bool, np.bool_))
+
+  if binary_image:
+    img = img.view(np.uint8)
+
   if tuple(factor) in ( (2,2), (2,2,1), (2,2,1,1) ) and not sparse:
     return tinybrain.accelerated.mode_pooling_2x2(img, num_mips=num_mips)
   elif tuple(factor) in ( (2,2,2), (2,2,2,1) ):
@@ -244,6 +249,10 @@ def downsample_segmentation(img, factor, sparse=False, num_mips=1):
     results.append(img)
 
   results = [ squeeze_dims(img, ndim) for img in results ]
+
+  if binary_image:
+    results = [ mip_img.view(bool) for mip_img in results ]
+
   return results
 
 def _downsample_segmentation(data, factor, sparse=False):

{tinybrain-1.7.0 → tinybrain-1.8.0}/tinybrain.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: tinybrain
-Version: 1.7.0
+Version: 1.8.0
 Summary: Image pyramid generation specialized for connectomics data types and procedures.
 Home-page: https://github.com/seung-lab/tinybrain/
 Author: William Silversmith

tinybrain-1.8.0/tinybrain.egg-info/pbr.json

@@ -0,0 +1 @@
+{"git_version": "c656201", "is_release": true}

tinybrain-1.7.0/tinybrain.egg-info/pbr.json

@@ -1 +0,0 @@
-{"git_version": "860d1fd", "is_release": true}