biomedisa 24.5.23__py3-none-any.whl → 24.8.1__py3-none-any.whl

biomedisa/features/remove_outlier.py

@@ -143,7 +143,7 @@ def fill(image, threshold=0.9):
     return image_i
 
 def main_helper(path_to_labels, img_id=None, friend_id=None, fill_holes=True,
-    clean_threshold=0.1, fill_threshold=0.9, remote=False, no_compression=False):
+    clean_threshold=0.1, fill_threshold=0.9, remote=False, compression=True):
 
     # django environment
     if img_id is not None:
@@ -151,12 +151,6 @@ def main_helper(path_to_labels, img_id=None, friend_id=None, fill_holes=True,
     else:
         django_env = False
 
-    # compression
-    if no_compression:
-        compression = False
-    else:
-        compression = True
-
     # final filenames
     filename, extension = os.path.splitext(path_to_labels)
     if extension == '.gz':
@@ -350,7 +344,7 @@ def init_remove_outlier(image_id, final_id, label_id, fill_holes=True):
             try:
                 main_helper(final.pic.path, img_id=image_id, friend_id=final.friend,
                     fill_holes=fill_holes, clean_threshold=label.delete_outliers, fill_threshold=label.fill_holes, remote=False,
-                    no_compression=(False if label.compression else True))
+                    compression=label.compression)
             except Exception as e:
                 print(traceback.format_exc())
 
@@ -377,7 +371,7 @@ if __name__ == '__main__':
                         help='Remove outliers, e.g. 0.5 means that objects smaller than 50 percent of the size of the largest object will be removed')
     parser.add_argument('-f', '--fill_threshold', type=float, default=0.9,
                         help='Fill holes, e.g. 0.5 means that all holes smaller than 50 percent of the entire label will be filled')
-    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('-iid','--img_id', type=str, default=None,
                         help='Image ID within django environment/browser version')

biomedisa/interpolation.py

@@ -42,7 +42,7 @@ class Biomedisa(object):
 
 def smart_interpolation(data, labelData, nbrw=10, sorw=4000, acwe=False, acwe_alpha=1.0, acwe_smooth=1, acwe_steps=3,
     path_to_data=None, path_to_labels=None, denoise=False, uncertainty=False, platform=None,
-    allaxis=False, ignore='none', only='all', smooth=0, no_compression=False, return_hits=False,
+    allaxis=False, ignore='none', only='all', smooth=0, compression=True, return_hits=False,
     img_id=None, label_id=None, remote=False, queue=0, clean=None, fill=None):
 
     freeze_support()
@@ -73,12 +73,6 @@ def smart_interpolation(data, labelData, nbrw=10, sorw=4000, acwe=False, acwe_al
         else:
             bm.django_env = False
 
-        # compression
-        if 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
@@ -149,19 +143,19 @@ def smart_interpolation(data, labelData, nbrw=10, sorw=4000, acwe=False, acwe_al
                 bm.path_to_acwe = filename + '.acwe' + bm.final_image_type
                 bm.path_to_uq = filename + '.uncertainty.tif'
 
-            # data type
-            if bm.data.dtype == 'uint8':
-                pass
-            elif bm.data.dtype == 'int8':
+            # data types
+            if bm.data.dtype == 'int8':
                 bm.data = bm.data.astype(np.int16)
                 bm.data += 128
                 bm.data = bm.data.astype(np.uint8)
-            else:
-                bm.data = bm.data.astype(float)
+            elif bm.data.dtype != 'uint8':
+                bm.data = bm.data.astype(np.float32)
                 bm.data -= np.amin(bm.data)
                 bm.data /= np.amax(bm.data)
                 bm.data *= 255.0
-                bm.data = bm.data.astype(np.float32)
+            if bm.labelData.dtype in ['uint32','int64','uint64']:
+                print(f'Warning: Potential label loss during conversion from {bm.labelData.dtype} to int32.')
+                bm.labelData = bm.labelData.astype(np.int32)
 
             # denoise image data
             if bm.denoise:
@@ -332,7 +326,7 @@ if __name__ == '__main__':
                         help='Smoothing steps of active contour')
     parser.add_argument('--acwe_steps', metavar='STEPS', type=int, default=3,
                         help='Iterations of active contour')
-    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('-allx', '--allaxis', action='store_true', default=False,
                         help='If pre-segmentation is not exlusively in xy-plane')

biomedisa/mesh.py

@@ -29,6 +29,7 @@
 
 import os
 import numpy as np
+import biomedisa
 from biomedisa.features.biomedisa_helper import load_data, unique_file_path
 from biomedisa.features.django_env import create_pid_object
 from vtk.util.numpy_support import vtk_to_numpy, numpy_to_vtk
@@ -167,8 +168,7 @@ def save_mesh(path_to_result, labels, x_res=1, y_res=1, z_res=1,
         mesh_final.attr[start:stop,0] = i+1
     mesh_final.save(path_to_result)
 
-def get_voxel_spacing(header, data, extension):
-
+def get_voxel_spacing(header, extension):
     if extension == '.am':
         # read header as string
         b = header[0].tobytes()
@@ -176,21 +176,23 @@ def get_voxel_spacing(header, data, extension):
             s = b.decode("utf-8")
         except:
             s = b.decode("latin1")
-
         # get physical size from image header
+        lattice = re.search('define Lattice (.*)\n', s)
         bounding_box = re.search('BoundingBox (.*),\n', s)
-        if bounding_box:
+        if bounding_box and lattice:
+            # get number of voxels
+            lattice = lattice.group(1)
+            xsh, ysh, zsh = lattice.split(' ')
+            xsh, ysh, zsh = float(xsh), float(ysh), float(zsh)
+            # get bounding box
             bounding_box = bounding_box.group(1)
             i0, i1, i2, i3, i4, i5 = bounding_box.split(' ')
-
-            # voxel spacing
-            zsh, ysh, xsh = data.shape
+            # calculate voxel spacing
             xres = (float(i1)-float(i0)) / xsh
             yres = (float(i3)-float(i2)) / ysh
             zres = (float(i5)-float(i4)) / zsh
         else:
             xres, yres, zres = 1, 1, 1
-
     elif extension in ['.hdr', '.mhd', '.mha', '.nrrd', '.nii', '.nii.gz']:
         xres, yres, zres = header.GetSpacing()
     elif extension == '.zip':
@@ -203,7 +205,6 @@ def get_voxel_spacing(header, data, extension):
     else:
         print('Warning: could not get voxel spacing. Using x_spacing, y_spacing, z_spacing = 1, 1, 1 instead.')
         xres, yres, zres = 1, 1, 1
-
     return xres, yres, zres
 
 def init_create_mesh(id):
@@ -324,7 +325,7 @@ def init_create_mesh(id):
                         log=1, imageType=None, shortfilename='Invalid label data.')
                 else:
                     # get voxel spacing
-                    xres, yres, zres = get_voxel_spacing(header, data, extension)
+                    xres, yres, zres = get_voxel_spacing(header, extension)
                     print(f'Voxel spacing: x_spacing, y_spacing, z_spacing = {xres}, {yres}, {zres}')
 
                     # create stl file
@@ -386,7 +387,7 @@ if __name__ == "__main__":
 
         # get voxel spacing
         if not all([bm.x_res, bm.y_res, bm.z_res]):
-            x_res, y_res, z_res = get_voxel_spacing(header, bm.labels, extension)
+            x_res, y_res, z_res = get_voxel_spacing(header, extension)
             if not bm.x_res:
                 bm.x_res = x_res
             if not bm.y_res:

{biomedisa-24.5.23.dist-info → biomedisa-24.8.1.dist-info}/METADATA

@@ -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.dist-info → biomedisa-24.8.1.dist-info}/RECORD

@@ -1,26 +1,26 @@
 biomedisa/__init__.py,sha256=hw4mzEjGFXm-vxus2DBfKFW0nKoG0ibL5SH6ShfchrY,1526
 biomedisa/__main__.py,sha256=a1--8vhtztWEloHVtbM43FZLCfrFo4BELgdsgtWE8ls,536
-biomedisa/deeplearning.py,sha256=UG5baX58CrO8YXe9pU6_Bp2OOvbC74LQw4S33HqM2iA,27828
-biomedisa/interpolation.py,sha256=R8UbBWt7vOuiQCPSeNIpEY0_yfQUg1oBfhAjXi91Hl4,17253
-biomedisa/mesh.py,sha256=glvpTN0PPByb5j2IbLCdWQtc5O4VT-Pwu3en8EaYyTo,15819
-biomedisa/features/DataGenerator.py,sha256=bGys6UZ0bnKb_k1Y3Spo6MNPk_goSAmptdZnI39smaw,12770
+biomedisa/deeplearning.py,sha256=Tfi1iSpsYi9RetgJpff_-mHx_VxlDybHZqTBJURwTBM,27970
+biomedisa/interpolation.py,sha256=i10aqwEl-wsVU_nQ-zyubhAs27NSKF4ial7LyhaBLv0,17273
+biomedisa/mesh.py,sha256=8-iuVsrfW5JovaMrAez7qSxv1LCU3eiqOdik0s0DV1w,16062
+biomedisa/features/DataGenerator.py,sha256=MYPSY9-ssMwPx9UOI_ZfE7_5rddOSn4aHbVQ0HtYQVA,12757
 biomedisa/features/DataGeneratorCrop.py,sha256=23R4Z-8tB1CsjYTYfhHGovlJpAny_q9OV9hq8kc2GJg,5454
 biomedisa/features/PredictDataGenerator.py,sha256=JH8SPGQm-Y7_Drec2fw3jBUupvpIkQ1FvkDXP7mUjDY,4074
 biomedisa/features/PredictDataGeneratorCrop.py,sha256=HF5tJbGtlJMHr7lMT9IiIdLG2CTjXstbKoOjlZJ93Is,3431
 biomedisa/features/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biomedisa/features/active_contour.py,sha256=n5_vAD8jvQjU6fQ6A9hxjSmtkLLo_1fl0S5q1H2pmVg,18096
+biomedisa/features/active_contour.py,sha256=FnPuvYck_KL4xYRFqwzm4Grdm288EdlcLFt88E0OtqA,17938
 biomedisa/features/assd.py,sha256=q9NUQXEoA4Pi3d8b5fmys615CWu06Sm0N9-OGwJOFnw,6537
-biomedisa/features/biomedisa_helper.py,sha256=iLbt4RpCU3EK51uiMefkM0321AgBdeLgrT-X4d--YJY,32250
-biomedisa/features/create_slices.py,sha256=tLDJmuJFN8teTiCYvMauExfVzT2ZUF28VcPXpo4sOsE,13001
-biomedisa/features/crop_helper.py,sha256=si72n9Q-C7U0cXYOD9Ux2UqIbZdXbZSOARBYDeqRggI,24533
+biomedisa/features/biomedisa_helper.py,sha256=oIsOmIJ8xUQVwgbzMgw65dXcZmzwePpFQoIdbgLTnF8,32727
+biomedisa/features/create_slices.py,sha256=uSDH1OcEYc5BFPZHSy3UpS4P2DuoVnxOZ-l7wmyT_Po,13108
+biomedisa/features/crop_helper.py,sha256=5do03z_DT13qWRR6IGtkFn4BNaw0mWmUXgg3Lk-U6QY,24597
 biomedisa/features/curvop_numba.py,sha256=AjKQJcUBoURTB8pq1HmugQYpBwBELthhcEu51_r_xPI,7049
 biomedisa/features/django_env.py,sha256=pdiPcBpqu1BWuyvh-palIGVwHFaY-leQ4Gatlbm8hIg,8942
-biomedisa/features/keras_helper.py,sha256=muPwb_W7O63exzWACJ4oLdAc-AQitcxLeNwgHvxyhuE,50488
+biomedisa/features/keras_helper.py,sha256=Y48N8VizQ2F7yrFzdUPOIFS19wm8fFWguQJqVFLVHWA,57637
 biomedisa/features/nc_reader.py,sha256=RoRMwu3ELSNfoV3qZtaT2OWACnXb2EhNFu_DAF1T93o,7406
 biomedisa/features/pid.py,sha256=Jmn1VIp0fBlgBrqZ-yUIQVVb5-NAxNBdibXALVr2PPI,2545
 biomedisa/features/process_image.py,sha256=VtS3fGDvglqJiiJLPK1toe76J58j914NJ8XQKg3CRwo,11091
 biomedisa/features/pycuda_test.py,sha256=UGAGIz_dgcCJkzjyCqnMlflp-WJPzpCtFQmE9C5DwIo,3275
-biomedisa/features/remove_outlier.py,sha256=XhbFPkazMmEUZiP0FERdCkrXaLhwO095x4wcn-B3SdU,16756
+biomedisa/features/remove_outlier.py,sha256=C2m-Wsw-n3q8Ft21SGNwEd3wDU_T1ghqQ5hldwU_rqI,16627
 biomedisa/features/split_volume.py,sha256=UgMpHhZPvH90xFo-mJ0Oc0tBXbrf8FQF0kzVySAlO8g,8917
 biomedisa/features/amira_to_np/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biomedisa/features/amira_to_np/amira_data_stream.py,sha256=JrZTyKP01CKDFB5d9BlGtSFwBgoAo0AJeAmn3pADH88,32618
@@ -37,8 +37,8 @@ biomedisa/features/random_walk/pyopencl_large.py,sha256=q79AxG3p3qFjxfiAZfUK9I5B
 biomedisa/features/random_walk/pyopencl_small.py,sha256=opNlS-qzOa9qWafBNJdvf6r1aRAFf7_JXf6ISDnkdXE,17068
 biomedisa/features/random_walk/rw_large.py,sha256=ZnITvk00Y11ZZlGuBRaJO1EwU0wYBdEwdpj9vvXCqF4,19805
 biomedisa/features/random_walk/rw_small.py,sha256=RPzZe24YrEwYelJukDjvqaoD_SyhgdriEi7uV3kZGXI,14881
-biomedisa-24.5.23.dist-info/LICENSE,sha256=sehayP6UhydNnmstfL4yFR3genMRdpuUh6uZVWJN1H0,14152
-biomedisa-24.5.23.dist-info/METADATA,sha256=XIEKdnTY54QTALYPtNambyN7NP7_e76S2Mo99Ubifv8,10475
-biomedisa-24.5.23.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-biomedisa-24.5.23.dist-info/top_level.txt,sha256=opsf1Eb4vCguPSxev4HHSeiUKCccT_C_RcUCdAYbHWQ,10
-biomedisa-24.5.23.dist-info/RECORD,,
+biomedisa-24.8.1.dist-info/LICENSE,sha256=sehayP6UhydNnmstfL4yFR3genMRdpuUh6uZVWJN1H0,14152
+biomedisa-24.8.1.dist-info/METADATA,sha256=GRHftPc4P9kZG5mgWe0KYpu-QMYWYBg2mSJqKuVitiE,10569
+biomedisa-24.8.1.dist-info/WHEEL,sha256=Mdi9PDNwEZptOjTlUcAth7XJDFtKrHYaQMPulZeBCiQ,91
+biomedisa-24.8.1.dist-info/top_level.txt,sha256=opsf1Eb4vCguPSxev4HHSeiUKCccT_C_RcUCdAYbHWQ,10
+biomedisa-24.8.1.dist-info/RECORD,,

{biomedisa-24.5.23.dist-info → biomedisa-24.8.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (73.0.1)
 Root-Is-Purelib: true
 Tag: py3-none-any