biomedisa 24.5.23__tar.gz → 24.8.1__tar.gz

{biomedisa-24.5.23 → biomedisa-24.8.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biomedisa
-Version: 24.5.23
+Version: 24.8.1
 Summary: Segmentation of 3D volumetric image data
 Author: Philipp Lösel
 Author-email: philipp.loesel@anu.edu.au
@@ -33,17 +33,20 @@ License-File: LICENSE
 - [License](#license)
 
 ## Overview
-Biomedisa (https://biomedisa.info) is a free and easy-to-use open-source application for segmenting large volumetric images, e.g. CT and MRI scans, developed at [The Australian National University CTLab](https://ctlab.anu.edu.au/). Biomedisa's semi-automated segmentation is based on a smart interpolation of sparsely pre-segmented slices, taking into account the complete underlying image data. In addition, Biomedisa enables deep learning for the fully automated segmentation of series of similar samples. It can be used in combination with segmentation tools such as 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).
+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 with compute capability 3.0 or higher or an Intel CPU
++ One or more NVIDIA GPUs with compute capability 3.0 or higher.
 
 ## Installation (command-line based)
-+ [Ubuntu 22.04 + CUDA + GPU (recommended)](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu2204_cuda11.8_gpu_cli.md)
-+ [Ubuntu 22.04 + OpenCL + CPU (smart interpolation only and very slow)](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu2204_opencl_cpu_cli.md)
-+ [Windows 10 + CUDA + GPU (recommended)](https://github.com/biomedisa/biomedisa/blob/master/README/windows10_cuda_gpu_cli.md)
-+ [Windows 10 + OpenCL + GPU (easy to install but lacks features like allaxis, smoothing, uncertainty, optimized GPU memory usage)](https://github.com/biomedisa/biomedisa/blob/master/README/windows10_opencl_gpu_cli.md)
-+ [Windows 10 + OpenCL + CPU (very slow)](https://github.com/biomedisa/biomedisa/blob/master/README/windows10_opencl_cpu_cli.md)
++ [Ubuntu 22.04 + Smart Interpolation](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu2204_interpolation_cli.md)
++ [Ubuntu 22.04 + Smart Interpolation + Deep Learning](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu2204_cuda11.8_gpu_cli.md)
++ [Windows 10 + Smart Interpolation + Deep Learning](https://github.com/biomedisa/biomedisa/blob/master/README/windows10_cuda_gpu_cli.md)
++ [Windows (WSL) + Smart Interpolation + Deep Learning](https://github.com/biomedisa/biomedisa/blob/master/README/windows_wsl.md)
+
+## Installation (3D Slicer extension)
++ [Ubuntu 22.04 + Smart Interpolation + Deep Learning](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu2204_cuda11.8_gpu_slicer.md)
++ [Windows 10 + Smart Interpolation](https://github.com/biomedisa/biomedisa/blob/master/README/windows10_cuda_gpu_slicer.md)
 
 ## Installation (browser based)
 + [Ubuntu 22.04](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu2204_cuda11.8.md)
@@ -52,6 +55,10 @@ Biomedisa (https://biomedisa.info) is a free and easy-to-use open-source applica
 + Download test data from our [gallery](https://biomedisa.info/gallery/)
 
 ## Revisions
+24.7.1
++ 3D Slicer extension
++ Prediction of large data block by block
+
 24.5.22
 + Pip is the preferred installation method
 + Commands, module names and imports have been changed to conform to the Pip standard
@@ -131,15 +138,14 @@ deep_learning(img_data, label_data, train=True, batch_size=12,
 ```
 
 #### Command-line based (training)
-Start training with a batch size of 12:
 ```
-python -m biomedisa.deeplearning C:\Users\%USERNAME%\Downloads\training_heart C:\Users\%USERNAME%\Downloads\training_heart_labels -t -bs=12
+python -m biomedisa.deeplearning C:\Users\%USERNAME%\Downloads\training_heart C:\Users\%USERNAME%\Downloads\training_heart_labels -t
 ```
 Monitor training progress using validation data:
 ```
 python -m biomedisa.deeplearning C:\Users\%USERNAME%\Downloads\training_heart C:\Users\%USERNAME%\Downloads\training_heart_labels -t -vi=C:\Users\%USERNAME%\Downloads\val_img -vl=C:\Users\%USERNAME%\Downloads\val_labels
 ```
-If running into ResourceExhaustedError due to out of memory (OOM), try to use a smaller batch size.
+If running into ResourceExhaustedError due to out of memory (OOM), try to use a smaller batch size (e.g. -bs=12).
 
 #### Python example (prediction)
 ```python
@@ -175,7 +181,7 @@ from biomedisa.mesh import get_voxel_spacing, save_mesh
 data, header, extension = load_data('final.Head5.am', return_extension=True)
 
 # get voxel spacing
-x_res, y_res, z_res = get_voxel_spacing(header, data, extension)
+x_res, y_res, z_res = get_voxel_spacing(header, extension)
 print(f'Voxel spacing: x_spacing, y_spacing, z_spacing = {x_res}, {y_res}, {z_res}')
 
 # save stl file

{biomedisa-24.5.23 → biomedisa-24.8.1}/README.md

@@ -17,17 +17,20 @@
 - [License](#license)
 
 ## Overview
-Biomedisa (https://biomedisa.info) is a free and easy-to-use open-source application for segmenting large volumetric images, e.g. CT and MRI scans, developed at [The Australian National University CTLab](https://ctlab.anu.edu.au/). Biomedisa's semi-automated segmentation is based on a smart interpolation of sparsely pre-segmented slices, taking into account the complete underlying image data. In addition, Biomedisa enables deep learning for the fully automated segmentation of series of similar samples. It can be used in combination with segmentation tools such as 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).
+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 with compute capability 3.0 or higher or an Intel CPU
++ One or more NVIDIA GPUs with compute capability 3.0 or higher.
 
 ## Installation (command-line based)
-+ [Ubuntu 22.04 + CUDA + GPU (recommended)](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu2204_cuda11.8_gpu_cli.md)
-+ [Ubuntu 22.04 + OpenCL + CPU (smart interpolation only and very slow)](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu2204_opencl_cpu_cli.md)
-+ [Windows 10 + CUDA + GPU (recommended)](https://github.com/biomedisa/biomedisa/blob/master/README/windows10_cuda_gpu_cli.md)
-+ [Windows 10 + OpenCL + GPU (easy to install but lacks features like allaxis, smoothing, uncertainty, optimized GPU memory usage)](https://github.com/biomedisa/biomedisa/blob/master/README/windows10_opencl_gpu_cli.md)
-+ [Windows 10 + OpenCL + CPU (very slow)](https://github.com/biomedisa/biomedisa/blob/master/README/windows10_opencl_cpu_cli.md)
++ [Ubuntu 22.04 + Smart Interpolation](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu2204_interpolation_cli.md)
++ [Ubuntu 22.04 + Smart Interpolation + Deep Learning](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu2204_cuda11.8_gpu_cli.md)
++ [Windows 10 + Smart Interpolation + Deep Learning](https://github.com/biomedisa/biomedisa/blob/master/README/windows10_cuda_gpu_cli.md)
++ [Windows (WSL) + Smart Interpolation + Deep Learning](https://github.com/biomedisa/biomedisa/blob/master/README/windows_wsl.md)
+
+## Installation (3D Slicer extension)
++ [Ubuntu 22.04 + Smart Interpolation + Deep Learning](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu2204_cuda11.8_gpu_slicer.md)
++ [Windows 10 + Smart Interpolation](https://github.com/biomedisa/biomedisa/blob/master/README/windows10_cuda_gpu_slicer.md)
 
 ## Installation (browser based)
 + [Ubuntu 22.04](https://github.com/biomedisa/biomedisa/blob/master/README/ubuntu2204_cuda11.8.md)
@@ -36,6 +39,10 @@ Biomedisa (https://biomedisa.info) is a free and easy-to-use open-source applica
 + Download test data from our [gallery](https://biomedisa.info/gallery/)
 
 ## Revisions
+24.7.1
++ 3D Slicer extension
++ Prediction of large data block by block
+
 24.5.22
 + Pip is the preferred installation method
 + Commands, module names and imports have been changed to conform to the Pip standard
@@ -115,15 +122,14 @@ deep_learning(img_data, label_data, train=True, batch_size=12,
 ```
 
 #### Command-line based (training)
-Start training with a batch size of 12:
 ```
-python -m biomedisa.deeplearning C:\Users\%USERNAME%\Downloads\training_heart C:\Users\%USERNAME%\Downloads\training_heart_labels -t -bs=12
+python -m biomedisa.deeplearning C:\Users\%USERNAME%\Downloads\training_heart C:\Users\%USERNAME%\Downloads\training_heart_labels -t
 ```
 Monitor training progress using validation data:
 ```
 python -m biomedisa.deeplearning C:\Users\%USERNAME%\Downloads\training_heart C:\Users\%USERNAME%\Downloads\training_heart_labels -t -vi=C:\Users\%USERNAME%\Downloads\val_img -vl=C:\Users\%USERNAME%\Downloads\val_labels
 ```
-If running into ResourceExhaustedError due to out of memory (OOM), try to use a smaller batch size.
+If running into ResourceExhaustedError due to out of memory (OOM), try to use a smaller batch size (e.g. -bs=12).
 
 #### Python example (prediction)
 ```python
@@ -159,7 +165,7 @@ from biomedisa.mesh import get_voxel_spacing, save_mesh
 data, header, extension = load_data('final.Head5.am', return_extension=True)
 
 # get voxel spacing
-x_res, y_res, z_res = get_voxel_spacing(header, data, extension)
+x_res, y_res, z_res = get_voxel_spacing(header, extension)
 print(f'Voxel spacing: x_spacing, y_spacing, z_spacing = {x_res}, {y_res}, {z_res}')
 
 # save stl file

{biomedisa-24.5.23 → biomedisa-24.8.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "biomedisa"
-version = "24.5.23"
+version = "24.8.1"
 authors = [
   { name="Philipp Lösel"}, {email="philipp.loesel@anu.edu.au" },
 ]

{biomedisa-24.5.23 → biomedisa-24.8.1}/src/biomedisa/deeplearning.py

@@ -65,11 +65,11 @@ def deep_learning(img_data, label_data=None, val_img_data=None, val_label_data=N
     path_to_images=None, path_to_labels=None, val_images=None, val_labels=None,
     path_to_model=None, predict=False, train=False, header_file=None,
     balance=False, crop_data=False, flip_x=False, flip_y=False, flip_z=False,
-    swapaxes=False, train_dice=False, val_dice=True, no_compression=False, ignore='none', only='all',
+    swapaxes=False, train_dice=False, val_dice=True, compression=True, ignore='none', only='all',
     network_filters='32-64-128-256-512', resnet=False, debug_cropping=False,
-    save_cropped=False, epochs=100, no_normalization=False, rotate=0.0, validation_split=0.0,
+    save_cropped=False, epochs=100, normalization=True, rotate=0.0, validation_split=0.0,
     learning_rate=0.01, stride_size=32, validation_stride_size=32, validation_freq=1,
-    batch_size=None, x_scale=256, y_scale=256, z_scale=256, no_scaling=False, early_stopping=0,
+    batch_size=None, x_scale=256, y_scale=256, z_scale=256, scaling=True, early_stopping=0,
     pretrained_model=None, fine_tune=False, workers=1, cropping_epochs=50,
     x_range=None, y_range=None, z_range=None, header=None, extension='.tif',
     img_header=None, img_extension='.tif', average_dice=False, django_env=False,
@@ -91,17 +91,13 @@ def deep_learning(img_data, label_data=None, val_img_data=None, val_label_data=N
     for arg in key_copy:
         bm.__dict__[arg] = locals()[arg]
 
-    # compression
-    if bm.no_compression:
-        bm.compression = False
-    else:
-        bm.compression = True
-
     # normalization
-    if bm.no_normalization:
+    bm.normalize = 1 if bm.normalization else 0
+
+    # use patch normalization instead of normalizing the entire volume
+    if not bm.scaling:
         bm.normalize = 0
-    else:
-        bm.normalize = 1
+        bm.patch_normalization = True
 
     # django environment
     if bm.django_env:
@@ -217,14 +213,19 @@ def deep_learning(img_data, label_data=None, val_img_data=None, val_label_data=N
         hf = h5py.File(bm.path_to_model, 'r')
         meta = hf.get('meta')
         configuration = meta.get('configuration')
-        channels, bm.x_scale, bm.y_scale, bm.z_scale, normalize, mu, sig = np.array(configuration)[:]
-        channels, bm.x_scale, bm.y_scale, bm.z_scale, normalize, mu, sig = int(channels), int(bm.x_scale), \
-                                int(bm.y_scale), int(bm.z_scale), int(normalize), float(mu), float(sig)
-        if '/meta/normalization' in hf:
-            normalization_parameters = np.array(meta.get('normalization'), dtype=float)
+        channels, bm.x_scale, bm.y_scale, bm.z_scale, bm.normalize, mu, sig = np.array(configuration)[:]
+        channels, bm.x_scale, bm.y_scale, bm.z_scale, bm.normalize, mu, sig = int(channels), int(bm.x_scale), \
+                                int(bm.y_scale), int(bm.z_scale), int(bm.normalize), float(mu), float(sig)
+        if 'normalization' in meta:
+            normalization_parameters = np.array(meta['normalization'], dtype=float)
         else:
             normalization_parameters = np.array([[mu],[sig]])
-        allLabels = np.array(meta.get('labels'))
+        bm.allLabels = np.array(meta.get('labels'))
+        if 'patch_normalization' in meta:
+            bm.patch_normalization = bool(meta['patch_normalization'][()])
+        if 'scaling' in meta:
+            bm.scaling = bool(meta['scaling'][()])
+
         # check if amira header is available in the network
         if header is None and meta.get('header') is not None:
             header = [np.array(meta.get('header'))]
@@ -290,16 +291,11 @@ def deep_learning(img_data, label_data=None, val_img_data=None, val_label_data=N
                     region_of_interest, cropped_volume = ch.crop_data(bm.path_to_image, bm.path_to_model, bm.path_to_cropped_image,
                         bm.batch_size, bm.debug_cropping, bm.save_cropped, img_data, bm.x_range, bm.y_range, bm.z_range)
 
-                # load prediction data
-                img, img_header, z_shape, y_shape, x_shape, region_of_interest, img_data = load_prediction_data(bm.path_to_image,
-                    channels, bm.x_scale, bm.y_scale, bm.z_scale, bm.no_scaling, normalize, normalization_parameters,
-                    region_of_interest, img_data, img_header)
-
                 # make prediction
-                results, bm = predict_semantic_segmentation(bm, img, bm.path_to_model,
-                    bm.z_patch, bm.y_patch, bm.x_patch, z_shape, y_shape, x_shape, bm.compression, header,
-                    img_header, bm.stride_size, allLabels, bm.batch_size, region_of_interest,
-                    bm.no_scaling, extension, img_data)
+                results, bm = predict_semantic_segmentation(bm,
+                    header, img_header,
+                    region_of_interest, extension, img_data,
+                    channels, normalization_parameters)
 
                 # results
                 if cropped_volume is not None:
@@ -403,7 +399,7 @@ if __name__ == '__main__':
                         help='Dice loss function')
     parser.add_argument('-ad','--average_dice', action='store_true', default=False,
                         help='Use averaged dice score of each label')
-    parser.add_argument('-nc', '--no_compression', action='store_true', default=False,
+    parser.add_argument('-nc', '--no-compression', dest='compression', action='store_false',
                         help='Disable compression of segmentation results')
     parser.add_argument('-i', '--ignore', type=str, default='none',
                         help='Ignore specific label(s), e.g. 2,5,6')
@@ -421,12 +417,12 @@ if __name__ == '__main__':
                         help='Epochs the network is trained')
     parser.add_argument('-ce','--cropping_epochs', type=int, default=50,
                         help='Epochs the network for auto-cropping is trained')
-    parser.add_argument('-nn','--no_normalization', action='store_true', default=False,
-                        help='Disable image normalization')
+    parser.add_argument('-nn','--no-normalization', dest='normalization', action='store_false',
+                        help='Disable normalization of 3D image volumes')
     parser.add_argument('-r','--rotate', type=float, default=0.0,
                         help='Randomly rotate during training')
     parser.add_argument('-vs','--validation_split', type=float, default=0.0,
-                        help='Percentage of data used for validation')
+                        help='Percentage of data used for training')
     parser.add_argument('-lr','--learning_rate', type=float, default=0.01,
                         help='Learning rate')
     parser.add_argument('-ss','--stride_size', metavar="[1-64]", type=int, choices=range(1,65), default=32,
@@ -447,7 +443,7 @@ if __name__ == '__main__':
                         help='Images and labels are scaled at y-axis to this size before training')
     parser.add_argument('-zs','--z_scale', type=int, default=256,
                         help='Images and labels are scaled at z-axis to this size before training')
-    parser.add_argument('-ns','--no_scaling', action='store_true', default=False,
+    parser.add_argument('-ns','--no-scaling', dest='scaling', action='store_false',
                         help='Do not resize image and label data')
     parser.add_argument('-es','--early_stopping', type=int, default=0,
                         help='Training is terminated when the accuracy has not increased in the epochs defined by this')
@@ -483,9 +479,18 @@ if __name__ == '__main__':
                         help='Processing queue when using a remote server')
     parser.add_argument('-hf','--header_file', type=str, metavar='PATH', default=None,
                         help='Location of header file')
+    parser.add_argument('-ext','--extension', type=str, default='.tif',
+                        help='Save data for example as NRRD file using --extension=".nrrd"')
     bm = parser.parse_args()
-
     bm.success = True
+
+    # prediction or training
+    if not any([bm.train, bm.predict]):
+        bm.predict = False
+        bm.train = True
+        if os.path.splitext(bm.path)[1] == '.h5':
+            bm.predict = True
+            bm.train = False
     if bm.predict:
         bm.path_to_labels = None
         bm.path_to_model = bm.path

{biomedisa-24.5.23 → biomedisa-24.8.1}/src/biomedisa/features/DataGenerator.py

@@ -286,7 +286,7 @@ class DataGenerator(tf.keras.utils.Sequence):
 
                 # patch normalization
                 if self.patch_normalization:
-                    tmp_X = np.copy(tmp_X, order='C')
+                    tmp_X = tmp_X.copy()
                     for c in range(self.n_channels):
                         tmp_X[:,:,:,c] -= np.mean(tmp_X[:,:,:,c])
                         tmp_X[:,:,:,c] /= max(np.std(tmp_X[:,:,:,c]), 1e-6)

{biomedisa-24.5.23 → biomedisa-24.8.1}/src/biomedisa/features/active_contour.py

@@ -106,7 +106,7 @@ def reduce_blocksize(raw, slices):
     return raw, slices, argmin_z, argmax_z, argmin_y, argmax_y, argmin_x, argmax_x
 
 def activeContour(data, labelData, alpha=1.0, smooth=1, steps=3,
-    path_to_data=None, path_to_labels=None, no_compression=False,
+    path_to_data=None, path_to_labels=None, compression=True,
     ignore='none', only='all', simple=False,
     img_id=None, friend_id=None, remote=False):
 
@@ -126,12 +126,6 @@ def activeContour(data, labelData, alpha=1.0, smooth=1, steps=3,
     else:
         bm.django_env = False
 
-    # compression
-    if bm.no_compression:
-        bm.compression = False
-    else:
-        bm.compression = True
-
     # disable file saving when called as a function
     if bm.data is not None:
         bm.path_to_data = None
@@ -374,8 +368,7 @@ def init_active_contour(image_id, friend_id, label_id, simple=False):
         else:
             try:
                 activeContour(None, None, path_to_data=image.pic.path, path_to_labels=friend.pic.path,
-                    alpha=label.ac_alpha, smooth=label.ac_smooth, steps=label.ac_steps,
-                    no_compression=(False if label.compression else True),
+                    alpha=label.ac_alpha, smooth=label.ac_smooth, steps=label.ac_steps, compression=label.compression,
                     simple=simple, img_id=image_id, friend_id=friend_id, remote=False)
             except Exception as e:
                 print(traceback.format_exc())
@@ -407,7 +400,7 @@ if __name__ == '__main__':
                         help='Number of smoothing steps')
     parser.add_argument('-st', '--steps', type=int, default=3,
                         help='Number of iterations')
-    parser.add_argument('-nc', '--no_compression', action='store_true', default=False,
+    parser.add_argument('-nc', '--no-compression', dest='compression', action='store_false',
                         help='Disable compression of segmentation results')
     parser.add_argument('-i', '--ignore', type=str, default='none',
                         help='Ignore specific label(s), e.g. 2,5,6')

{biomedisa-24.5.23 → biomedisa-24.8.1}/src/biomedisa/features/biomedisa_helper.py

@@ -317,19 +317,23 @@ def load_data(path_to_data, process='None', return_extension=False):
                         data, header = None, None
                 else:
                     try:
-                        # remove unreadable files or directories
-                        for name in files:
-                            if os.path.isfile(name):
+                        # load data slice by slice
+                        file_names = []
+                        img_slices = []
+                        header = []
+                        files.sort()
+                        for file_name in files:
+                            if os.path.isfile(file_name):
                                 try:
-                                    img, _ = load(name)
+                                    img, img_header = load(file_name)
+                                    file_names.append(file_name)
+                                    img_slices.append(img)
+                                    header.append(img_header)
                                 except:
-                                    files.remove(name)
-                            else:
-                                files.remove(name)
-                        files.sort()
+                                    pass
 
                         # get data size
-                        img, _ = load(files[0])
+                        img = img_slices[0]
                         if len(img.shape)==3:
                             ysh, xsh, csh = img.shape[0], img.shape[1], img.shape[2]
                             channel = 'last'
@@ -340,11 +344,9 @@ def load_data(path_to_data, process='None', return_extension=False):
                             ysh, xsh = img.shape[0], img.shape[1]
                             csh, channel = 0, None
 
-                        # load data slice by slice
-                        data = np.empty((len(files), ysh, xsh), dtype=img.dtype)
-                        header, image_data_shape = [], []
-                        for k, file_name in enumerate(files):
-                            img, img_header = load(file_name)
+                        # create 3D volume
+                        data = np.empty((len(file_names), ysh, xsh), dtype=img.dtype)
+                        for k, img in enumerate(img_slices):
                             if csh==3:
                                 img = rgb2gray(img, channel)
                             elif csh==1 and channel=='last':
@@ -352,8 +354,7 @@ def load_data(path_to_data, process='None', return_extension=False):
                             elif csh==1 and channel=='first':
                                 img = img[0,:,:]
                             data[k] = img
-                            header.append(img_header)
-                        header = [header, files, data.dtype]
+                        header = [header, file_names, data.dtype]
                         data = np.swapaxes(data, 1, 2)
                         data = np.copy(data, order='C')
                     except Exception as e:
@@ -415,25 +416,33 @@ def pre_processing(bm):
     if bm.labelData is None:
         return _error_(bm, 'Invalid label data.')
 
+    # dimension errors
     if len(bm.labelData.shape) != 3:
-        return _error_(bm, 'Label must be three-dimensional.')
-
+        return _error_(bm, 'Label data must be three-dimensional.')
     if bm.data.shape != bm.labelData.shape:
-        return _error_(bm, 'Image and label must have the same x,y,z-dimensions.')
+        return _error_(bm, 'Image and label data must have the same x,y,z-dimensions.')
+
+    # label data type
+    if bm.labelData.dtype in ['float16','float32','float64']:
+        if bm.django_env:
+            return _error_(bm, 'Label data must be of integer type.')
+        print(f'Warning: Potential label loss during conversion from {bm.labelData.dtype} to int32.')
+        bm.labelData = bm.labelData.astype(np.int32)
 
     # get labels
     bm.allLabels = np.unique(bm.labelData)
     index = np.argwhere(bm.allLabels<0)
     bm.allLabels = np.delete(bm.allLabels, index)
 
-    if bm.django_env and np.any(bm.allLabels > 255):
-        return _error_(bm, 'No labels higher than 255 allowed.')
-
+    # labels greater than 255
     if np.any(bm.allLabels > 255):
-        bm.labelData[bm.labelData > 255] = 0
-        index = np.argwhere(bm.allLabels > 255)
-        bm.allLabels = np.delete(bm.allLabels, index)
-        print('Warning: Only labels <=255 are allowed. Labels higher than 255 will be removed.')
+        if bm.django_env:
+            return _error_(bm, 'No labels greater than 255 allowed.')
+        else:
+            bm.labelData[bm.labelData > 255] = 0
+            index = np.argwhere(bm.allLabels > 255)
+            bm.allLabels = np.delete(bm.allLabels, index)
+            print('Warning: Only labels <=255 are allowed. Labels greater than 255 will be removed.')
 
     # add background label if not existing
     if not np.any(bm.allLabels==0):
@@ -485,7 +494,8 @@ def save_data(path_to_final, final, header=None, final_image_type=None, compress
         np_to_nc(path_to_final, final, header)
     elif final_image_type in ['.hdr', '.mhd', '.mha', '.nrrd', '.nii', '.nii.gz']:
         simg = sitk.GetImageFromArray(final)
-        simg.CopyInformation(header)
+        if header is not None:
+            simg.CopyInformation(header)
         sitk.WriteImage(simg, path_to_final, useCompression=compress)
     elif final_image_type in ['.zip', 'directory', '']:
         with tempfile.TemporaryDirectory() as temp_dir:

{biomedisa-24.5.23 → biomedisa-24.8.1}/src/biomedisa/features/create_slices.py

@@ -151,6 +151,7 @@ def create_slices(path_to_data, path_to_label, on_site=False):
             # increase contrast
             raw = img_to_uint8(raw)
             raw = contrast(raw)
+            zsh, ysh, xsh = raw.shape
 
             # create slices for slice viewer
             if not os.path.isdir(path_to_slices):
@@ -160,9 +161,9 @@ def create_slices(path_to_data, path_to_label, on_site=False):
                 os.chmod(path_to_slices, 0o770)
 
                 # save slices
-                for k in range(raw.shape[0]):
+                for k in range(zsh):
                     im = Image.fromarray(raw[k])
-                    im.save(path_to_slices + f'/{k}.png')
+                    im.save(path_to_slices + '/slice_' + str(k).zfill(len(str(zsh-1))) + '.png')
 
             if path_to_label and not os.path.isdir(path_to_label_slices):
 
@@ -263,7 +264,7 @@ def create_slices(path_to_data, path_to_label, on_site=False):
 
                         # save slice
                         im = Image.fromarray(out)
-                        im.save(path_to_label_slices + f'/{k}.png')
+                        im.save(path_to_label_slices + '/slice_' + str(k).zfill(len(str(zsh-1))) + '.png')
 
     except Exception as e:
         print(e)

{biomedisa-24.5.23 → biomedisa-24.8.1}/src/biomedisa/features/crop_helper.py

@@ -542,7 +542,8 @@ def load_and_train(normalize,path_to_img,path_to_labels,path_to_model,
                 cropping_weights.append(arr)
 
     # configuration data
-    cropping_config = np.array([channels, x_scale, y_scale, z_scale, normalize, 0, 1])
+    cropping_config = np.array([channels, x_scale, y_scale, z_scale, normalize,
+        normalization_parameters[0,0], normalization_parameters[1,0]])
 
     return cropping_weights, cropping_config, normalization_parameters