biomedisa 25.6.1__tar.gz → 25.7.1__tar.gz

{biomedisa-25.6.1 → biomedisa-25.7.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biomedisa
-Version: 25.6.1
+Version: 25.7.1
 Summary: Segmentation of 3D volumetric image data
 Author: Philipp Lösel
 Author-email: philipp.loesel@anu.edu.au
@@ -37,13 +37,14 @@ Dynamic: license-file
 Biomedisa (https://biomedisa.info) is a free and easy-to-use open-source application for segmenting large 3D volumetric images such as CT and MRI scans, developed at [The Australian National University CTLab](https://ctlab.anu.edu.au/). Biomedisa's smart interpolation of sparsely pre-segmented slices enables accurate semi-automated segmentation by considering the complete underlying image data. Additionally, Biomedisa enables deep learning for fully automated segmentation across similar samples and structures. It is compatible with segmentation tools like Amira/Avizo, ImageJ/Fiji, and 3D Slicer. If you are using Biomedisa or the data for your research please cite: Lösel, P.D. et al. [Introducing Biomedisa as an open-source online platform for biomedical image segmentation.](https://www.nature.com/articles/s41467-020-19303-w) *Nat. Commun.* **11**, 5577 (2020).
 
 ## Hardware Requirements
-+ One or more NVIDIA GPUs
++ One or more NVIDIA, AMD, or Intel GPUs
 
 ## Installation (command-line based)
 + [Ubuntu 22/24 + Smart Interpolation](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu_interpolation_cli.md)
 + [Ubuntu 22/24 + Deep Learning](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu_deeplearning_cli.md)
 + [Ubuntu 22/24 + Smart Interpolation + Deep Learning](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu_cli.md)
-+ [Windows 10/11 + Smart Interpolation + Deep Learning](https://github.com/biomedisa/biomedisa/blob/master/README/windows_wsl.md)
++ [Windows (WSL) + Smart Interpolation + Deep Learning ("advanced")](https://github.com/biomedisa/biomedisa/blob/master/README/windows_wsl.md)
++ [Windows 10/11 + Smart Interpolation (NVIDIA, AMD, Intel) ("simple")](https://github.com/biomedisa/biomedisa/blob/master/README/windows_interpolation.md)
 
 ## Installation (3D Slicer extension)
 + [Ubuntu 22/24](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu_slicer.md)

{biomedisa-25.6.1 → biomedisa-25.7.1}/README.md

@@ -20,13 +20,14 @@
 Biomedisa (https://biomedisa.info) is a free and easy-to-use open-source application for segmenting large 3D volumetric images such as CT and MRI scans, developed at [The Australian National University CTLab](https://ctlab.anu.edu.au/). Biomedisa's smart interpolation of sparsely pre-segmented slices enables accurate semi-automated segmentation by considering the complete underlying image data. Additionally, Biomedisa enables deep learning for fully automated segmentation across similar samples and structures. It is compatible with segmentation tools like Amira/Avizo, ImageJ/Fiji, and 3D Slicer. If you are using Biomedisa or the data for your research please cite: Lösel, P.D. et al. [Introducing Biomedisa as an open-source online platform for biomedical image segmentation.](https://www.nature.com/articles/s41467-020-19303-w) *Nat. Commun.* **11**, 5577 (2020).
 
 ## Hardware Requirements
-+ One or more NVIDIA GPUs
++ One or more NVIDIA, AMD, or Intel GPUs
 
 ## Installation (command-line based)
 + [Ubuntu 22/24 + Smart Interpolation](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu_interpolation_cli.md)
 + [Ubuntu 22/24 + Deep Learning](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu_deeplearning_cli.md)
 + [Ubuntu 22/24 + Smart Interpolation + Deep Learning](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu_cli.md)
-+ [Windows 10/11 + Smart Interpolation + Deep Learning](https://github.com/biomedisa/biomedisa/blob/master/README/windows_wsl.md)
++ [Windows (WSL) + Smart Interpolation + Deep Learning ("advanced")](https://github.com/biomedisa/biomedisa/blob/master/README/windows_wsl.md)
++ [Windows 10/11 + Smart Interpolation (NVIDIA, AMD, Intel) ("simple")](https://github.com/biomedisa/biomedisa/blob/master/README/windows_interpolation.md)
 
 ## Installation (3D Slicer extension)
 + [Ubuntu 22/24](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu_slicer.md)

{biomedisa-25.6.1 → biomedisa-25.7.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "biomedisa"
-version = "25.6.1"
+version = "25.7.1"
 authors = [
   { name="Philipp Lösel"}, {email="philipp.loesel@anu.edu.au" },
 ]

{biomedisa-25.6.1 → biomedisa-25.7.1}/src/biomedisa/features/biomedisa_helper.py

@@ -32,6 +32,7 @@ from biomedisa.features.amira_to_np.amira_helper import amira_to_np, np_to_amira
 from biomedisa.features.nc_reader import nc_to_np, np_to_nc
 from tifffile import imread, imwrite
 from medpy.io import load, save
+from skimage import io
 import SimpleITK as sitk
 from PIL import Image
 import numpy as np
@@ -67,23 +68,26 @@ def welford_mean_std(arr):
 
 # determine all values and their count from an array
 def unique(arr, return_counts=False):
-    try:
-        arr = arr.ravel()
-        counts = np.zeros(np.amax(arr)+1, dtype=int)
-        @numba.jit(nopython=True)
-        def __unique__(arr, size, counts):
-            for k in range(size):
-                counts[arr[k]] += 1
-            return counts
-        counts = __unique__(arr, arr.size, counts)
-        labels = np.where(counts)[0]
-        if return_counts:
-            return labels, counts[labels]
-        else:
-            return labels
-    except Exception as e:
-        print(f"Error: {e}")
-        return None
+    if np.issubdtype(arr.dtype, np.integer) and np.all(arr >= 0):
+        try:
+            arr = arr.ravel()
+            counts = np.zeros(np.amax(arr)+1, dtype=int)
+            @numba.jit(nopython=True)
+            def __unique__(arr, size, counts):
+                for k in range(size):
+                    counts[arr[k]] += 1
+                return counts
+            counts = __unique__(arr, arr.size, counts)
+            labels = np.where(counts)[0]
+            if return_counts:
+                return labels, counts[labels]
+            else:
+                return labels
+        except Exception as e:
+            print(f"Error: {e}")
+            return None
+    else:
+        return np.unique(arr, return_counts=return_counts)
 
 # create a unique filename
 def unique_file_path(path, dir_path=biomedisa.BASE_DIR+'/private_storage/'):
@@ -273,6 +277,10 @@ def recursive_file_permissions(path_to_dir):
         except:
             pass
 
+def natural_key(string):
+    # Split the string into parts of digits and non-digits
+    return [int(s) if s.isdigit() else s.lower() for s in re.split(r'(\d+)', string)]
+
 def load_data(path_to_data, process='None', return_extension=False):
 
     if not os.path.exists(path_to_data):
@@ -354,7 +362,7 @@ def load_data(path_to_data, process='None', return_extension=False):
                         file_names = []
                         img_slices = []
                         header = []
-                        files.sort()
+                        files.sort(key=natural_key)
                         for file_name in files:
                             if os.path.isfile(file_name):
                                 try:
@@ -362,8 +370,16 @@ def load_data(path_to_data, process='None', return_extension=False):
                                     file_names.append(file_name)
                                     img_slices.append(img)
                                     header.append(img_header)
-                                except:
-                                    pass
+                                except RuntimeError as e:
+                                    # Check for 64-bit TIFF error
+                                    if "Unable to read tiff file" in str(e) and "64-bit samples" in str(e):
+                                        try:
+                                            img = io.imread(file_name)
+                                            file_names.append(file_name)
+                                            img_slices.append(img)
+                                            header.append(None)
+                                        except:
+                                            pass
 
                         # get data size
                         img = img_slices[0]

{biomedisa-25.6.1 → biomedisa-25.7.1}/src/biomedisa/features/keras_helper.py

@@ -1643,7 +1643,7 @@ def predict_segmentation(bm, region_of_interest, channels, normalization_paramet
         if bm.return_probs and not load_blockwise:
             probabilities = scale_probabilities(final)
             if bm.scaling:
-                probabilities = img_resize(probabilities, z_shape, y_shape, x_shape)
+                probabilities = img_resize(probabilities, z_shape, y_shape, x_shape, interpolation=cv2.INTER_LINEAR)
             if np.any(region_of_interest):
                 min_z,max_z,min_y,max_y,min_x,max_x,original_zsh,original_ysh,original_xsh = region_of_interest[:]
                 tmp = np.zeros((original_zsh, original_ysh, original_xsh, nb_labels), dtype=np.float32)

{biomedisa-25.6.1 → biomedisa-25.7.1}/src/biomedisa/features/random_walk/pyopencl_large.py

@@ -259,7 +259,7 @@ def walk(comm, raw, slices, indices, nbrw, sorw, blockmin, blockmax,
     # allocate device memory or use subdomains
     memory_error = False
     subdomains = False
-    if zsh * ysh * xsh > 42e8 or platform.split('_')[-1] == 'GPU':
+    if zsh * ysh * xsh > 42e8:# or platform.split('_')[-1] == 'GPU':
         if zsh * ysh * xsh > 42e8:
             print('Warning: Volume indexes exceed unsigned long int range. The volume is splitted into subdomains.')
         else:

{biomedisa-25.6.1 → biomedisa-25.7.1}/src/biomedisa/features/random_walk/pyopencl_small.py

@@ -98,9 +98,9 @@ def _walk_on_current_gpu(raw, slices, allLabels, indices, nbrw, sorw, name, ctx,
     segment_cl = cl.Buffer(ctx, mf.READ_ONLY | mf.COPY_HOST_PTR, hostbuf=np.int32(0))
 
     # block and grid size
-    #block = (1, 32, 32)
-    #x_grid = ((xsh // 32) + 1)*32
-    #y_grid = ((ysh // 32) + 1)*32
+    #block = (1, 16, 16)
+    #x_grid = ((xsh // 16) + 1)*16
+    #y_grid = ((ysh // 16) + 1)*16
     #grid = (slshape, y_grid, x_grid)
 
     block = None

{biomedisa-25.6.1 → biomedisa-25.7.1}/src/biomedisa.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biomedisa
-Version: 25.6.1
+Version: 25.7.1
 Summary: Segmentation of 3D volumetric image data
 Author: Philipp Lösel
 Author-email: philipp.loesel@anu.edu.au
@@ -37,13 +37,14 @@ Dynamic: license-file
 Biomedisa (https://biomedisa.info) is a free and easy-to-use open-source application for segmenting large 3D volumetric images such as CT and MRI scans, developed at [The Australian National University CTLab](https://ctlab.anu.edu.au/). Biomedisa's smart interpolation of sparsely pre-segmented slices enables accurate semi-automated segmentation by considering the complete underlying image data. Additionally, Biomedisa enables deep learning for fully automated segmentation across similar samples and structures. It is compatible with segmentation tools like Amira/Avizo, ImageJ/Fiji, and 3D Slicer. If you are using Biomedisa or the data for your research please cite: Lösel, P.D. et al. [Introducing Biomedisa as an open-source online platform for biomedical image segmentation.](https://www.nature.com/articles/s41467-020-19303-w) *Nat. Commun.* **11**, 5577 (2020).
 
 ## Hardware Requirements
-+ One or more NVIDIA GPUs
++ One or more NVIDIA, AMD, or Intel GPUs
 
 ## Installation (command-line based)
 + [Ubuntu 22/24 + Smart Interpolation](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu_interpolation_cli.md)
 + [Ubuntu 22/24 + Deep Learning](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu_deeplearning_cli.md)
 + [Ubuntu 22/24 + Smart Interpolation + Deep Learning](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu_cli.md)
-+ [Windows 10/11 + Smart Interpolation + Deep Learning](https://github.com/biomedisa/biomedisa/blob/master/README/windows_wsl.md)
++ [Windows (WSL) + Smart Interpolation + Deep Learning ("advanced")](https://github.com/biomedisa/biomedisa/blob/master/README/windows_wsl.md)
++ [Windows 10/11 + Smart Interpolation (NVIDIA, AMD, Intel) ("simple")](https://github.com/biomedisa/biomedisa/blob/master/README/windows_interpolation.md)
 
 ## Installation (3D Slicer extension)
 + [Ubuntu 22/24](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu_slicer.md)