biomedisa 2024.5.19__py3-none-any.whl → 2024.5.20__py3-none-any.whl

biomedisa/{biomedisa_features → features}/random_walk/pyopencl_large.py

@@ -1,6 +1,6 @@
 ##########################################################################
 ##                                                                      ##
-##  Copyright (c) 2024 Philipp Lösel. All rights reserved.              ##
+##  Copyright (c) 2019-2024 Philipp Lösel. All rights reserved.         ##
 ##                                                                      ##
 ##  This file is part of the open source project biomedisa.             ##
 ##                                                                      ##

biomedisa/{biomedisa_features → features}/random_walk/pyopencl_small.py

@@ -1,6 +1,6 @@
 ##########################################################################
 ##                                                                      ##
-##  Copyright (c) 2023 Philipp Lösel. All rights reserved.              ##
+##  Copyright (c) 2019-2024 Philipp Lösel. All rights reserved.         ##
 ##                                                                      ##
 ##  This file is part of the open source project biomedisa.             ##
 ##                                                                      ##

biomedisa/{biomedisa_features → features}/random_walk/rw_large.py

@@ -1,6 +1,6 @@
 ##########################################################################
 ##                                                                      ##
-##  Copyright (c) 2024 Philipp Lösel. All rights reserved.              ##
+##  Copyright (c) 2019-2024 Philipp Lösel. All rights reserved.         ##
 ##                                                                      ##
 ##  This file is part of the open source project biomedisa.             ##
 ##                                                                      ##
@@ -26,9 +26,9 @@
 ##                                                                      ##
 ##########################################################################
 
-from biomedisa_features.remove_outlier import clean, fill
-from biomedisa_features.active_contour import activeContour
-from biomedisa_features.biomedisa_helper import (_get_device, save_data, _error_, unique_file_path,
+from biomedisa.features.remove_outlier import clean, fill
+from biomedisa.features.active_contour import activeContour
+from biomedisa.features.biomedisa_helper import (_get_device, save_data, _error_, unique_file_path,
     splitlargedata, read_labeled_slices_allx_large, read_labeled_slices_large, sendToChildLarge,
     Dice_score)
 from mpi4py import MPI
@@ -135,12 +135,12 @@ def _diffusion_child(comm, bm=None):
                     dev = cuda.Device(rank)
                     ctx, queue = dev.make_context(), None
                     if bm.allaxis:
-                        from biomedisa_features.random_walk.pycuda_large_allx import walk
+                        from biomedisa.features.random_walk.pycuda_large_allx import walk
                     else:
-                        from biomedisa_features.random_walk.pycuda_large import walk
+                        from biomedisa.features.random_walk.pycuda_large import walk
                 else:
                     ctx, queue = _get_device(bm.platform, rank)
-                    from biomedisa_features.random_walk.pyopencl_large import walk
+                    from biomedisa.features.random_walk.pyopencl_large import walk
 
                 # run random walks
                 tic = time.time()
@@ -279,7 +279,7 @@ def _diffusion_child(comm, bm=None):
             # post processing
             if bm.django_env:
                 from biomedisa_app.config import config
-                from biomedisa_features.django_env import post_processing
+                from biomedisa.features.django_env import post_processing
                 post_processing(bm.path_to_final, time_str, config['SERVER_ALIAS'], bm.remote, bm.queue,
                     dice=dice, uncertainty=bm.uncertainty, smooth=bm.smooth,
                     path_to_uq=bm.path_to_uq, path_to_smooth=bm.path_to_smooth,
@@ -341,12 +341,12 @@ def _diffusion_child(comm, bm=None):
             dev = cuda.Device(rank % cuda.Device.count())
             ctx, queue = dev.make_context(), None
             if allx:
-                from biomedisa_features.random_walk.pycuda_large_allx import walk
+                from biomedisa.features.random_walk.pycuda_large_allx import walk
             else:
-                from biomedisa_features.random_walk.pycuda_large import walk
+                from biomedisa.features.random_walk.pycuda_large import walk
         else:
             ctx, queue = _get_device(platform, rank)
-            from biomedisa_features.random_walk.pyopencl_large import walk
+            from biomedisa.features.random_walk.pyopencl_large import walk
 
         # run random walks
         tic = time.time()

biomedisa/{biomedisa_features → features}/random_walk/rw_small.py

@@ -1,6 +1,6 @@
 ##########################################################################
 ##                                                                      ##
-##  Copyright (c) 2024 Philipp Lösel. All rights reserved.              ##
+##  Copyright (c) 2019-2024 Philipp Lösel. All rights reserved.         ##
 ##                                                                      ##
 ##  This file is part of the open source project biomedisa.             ##
 ##                                                                      ##
@@ -26,9 +26,9 @@
 ##                                                                      ##
 ##########################################################################
 
-from biomedisa_features.remove_outlier import clean, fill
-from biomedisa_features.active_contour import activeContour
-from biomedisa_features.biomedisa_helper import (_get_device, save_data, unique_file_path,
+from biomedisa.features.remove_outlier import clean, fill
+from biomedisa.features.active_contour import activeContour
+from biomedisa.features.biomedisa_helper import (_get_device, save_data, unique_file_path,
     sendToChild, _split_indices, get_labels, Dice_score)
 from mpi4py import MPI
 import numpy as np
@@ -63,18 +63,18 @@ def _diffusion_child(comm, bm=None):
         if bm.platform == 'cuda':
             import pycuda.driver as cuda
             import pycuda.gpuarray as gpuarray
-            from biomedisa_features.random_walk.gpu_kernels import (_build_kernel_uncertainty, 
+            from biomedisa.features.random_walk.gpu_kernels import (_build_kernel_uncertainty, 
                         _build_kernel_max, _build_update_gpu, _build_curvature_gpu)
             cuda.init()
             dev = cuda.Device(rank)
             ctx, queue = dev.make_context(), None
             if bm.allaxis:
-                from biomedisa_features.random_walk.pycuda_small_allx import walk
+                from biomedisa.features.random_walk.pycuda_small_allx import walk
             else:
-                from biomedisa_features.random_walk.pycuda_small import walk
+                from biomedisa.features.random_walk.pycuda_small import walk
         else:
             ctx, queue = _get_device(bm.platform, rank)
-            from biomedisa_features.random_walk.pyopencl_small import walk
+            from biomedisa.features.random_walk.pyopencl_small import walk
 
         # run random walks
         tic = time.time()
@@ -238,7 +238,7 @@ def _diffusion_child(comm, bm=None):
         # post processing
         if bm.django_env:
             from biomedisa_app.config import config
-            from biomedisa_features.django_env import post_processing
+            from biomedisa.features.django_env import post_processing
             post_processing(bm.path_to_final, time_str, config['SERVER_ALIAS'], bm.remote, bm.queue,
                 dice=dice, uncertainty=bm.uncertainty, smooth=bm.smooth,
                 path_to_uq=bm.path_to_uq, path_to_smooth=bm.path_to_smooth,
@@ -281,12 +281,12 @@ def _diffusion_child(comm, bm=None):
             dev = cuda.Device(rank % cuda.Device.count())
             ctx, queue = dev.make_context(), None
             if allx:
-                from biomedisa_features.random_walk.pycuda_small_allx import walk
+                from biomedisa.features.random_walk.pycuda_small_allx import walk
             else:
-                from biomedisa_features.random_walk.pycuda_small import walk
+                from biomedisa.features.random_walk.pycuda_small import walk
         else:
             ctx, queue = _get_device(platform, rank)
-            from biomedisa_features.random_walk.pyopencl_small import walk
+            from biomedisa.features.random_walk.pyopencl_small import walk
 
         # run random walks
         tic = time.time()

biomedisa/{biomedisa_features → features}/remove_outlier.py

@@ -1,7 +1,7 @@
 #!/usr/bin/python3
 ##########################################################################
 ##                                                                      ##
-##  Copyright (c) 2024 Philipp Lösel. All rights reserved.              ##
+##  Copyright (c) 2019-2024 Philipp Lösel. All rights reserved.         ##
 ##                                                                      ##
 ##  This file is part of the open source project biomedisa.             ##
 ##                                                                      ##
@@ -27,12 +27,9 @@
 ##                                                                      ##
 ##########################################################################
 
-import sys, os
-BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
-if not BASE_DIR in sys.path:
-    sys.path.append(BASE_DIR)
+import os
 import biomedisa
-from biomedisa_features.biomedisa_helper import (load_data, save_data,
+from biomedisa.features.biomedisa_helper import (load_data, save_data,
     unique_file_path, silent_remove)
 import numpy as np
 from scipy import ndimage
@@ -195,13 +192,13 @@ def main_helper(path_to_labels, img_id=None, friend_id=None, fill_holes=True,
 
 def post_processing(path_to_cleaned, path_to_filled, path_to_cleaned_filled, img_id=None, friend_id=None, fill_holes=False, remote=False):
     if remote:
-        with open(BASE_DIR + '/log/config_6', 'w') as configfile:
+        with open(biomedisa.BASE_DIR + '/log/config_6', 'w') as configfile:
             print(path_to_cleaned, path_to_filled, path_to_cleaned_filled, file=configfile)
     else:
         import django
         django.setup()
         from biomedisa_app.models import Upload
-        from biomedisa_features.create_slices import create_slices
+        from biomedisa.features.create_slices import create_slices
         from redis import Redis
         from rq import Queue
 
@@ -279,7 +276,7 @@ def init_remove_outlier(image_id, final_id, label_id, fill_holes=True):
 
     # get host information
     host = ''
-    host_base = BASE_DIR
+    host_base = biomedisa.BASE_DIR
     subhost, qsub_pid = None, None
     if 'REMOTE_QUEUE_HOST' in config:
         host = config['REMOTE_QUEUE_HOST']
@@ -292,7 +289,7 @@ def init_remove_outlier(image_id, final_id, label_id, fill_holes=True):
         if host:
 
             # command
-            cmd = ['python3', host_base+'/biomedisa_features/remove_outlier.py', final.pic.path.replace(BASE_DIR,host_base)]
+            cmd = ['python3', host_base+'/biomedisa/features/remove_outlier.py', final.pic.path.replace(biomedisa.BASE_DIR,host_base)]
             cmd += [f'-iid={image.id}', f'-fid={final.friend}', '-r']
 
             # command (append only on demand)
@@ -309,7 +306,7 @@ def init_remove_outlier(image_id, final_id, label_id, fill_holes=True):
             subprocess.Popen(['ssh', host, 'mkdir', '-p', host_base+'/private_storage/images/'+image.user.username]).wait()
 
             # send data to host
-            success = send_data_to_host(final.pic.path, host+':'+final.pic.path.replace(BASE_DIR,host_base))
+            success = send_data_to_host(final.pic.path, host+':'+final.pic.path.replace(biomedisa.BASE_DIR,host_base))
 
             if success==0:
 
@@ -325,16 +322,16 @@ def init_remove_outlier(image_id, final_id, label_id, fill_holes=True):
                 subprocess.Popen(cmd).wait()
 
                 # config
-                success = subprocess.Popen(['scp', host+':'+host_base+'/log/config_6', BASE_DIR+'/log/config_6']).wait()
+                success = subprocess.Popen(['scp', host+':'+host_base+'/log/config_6', biomedisa.BASE_DIR+'/log/config_6']).wait()
 
                 if success==0:
-                    with open(BASE_DIR + '/log/config_6', 'r') as configfile:
+                    with open(biomedisa.BASE_DIR + '/log/config_6', 'r') as configfile:
                         cleaned_on_host, filled_on_host, cleaned_filled_on_host = configfile.read().split()
 
                     # local file names
-                    path_to_cleaned = unique_file_path(cleaned_on_host.replace(host_base,BASE_DIR))
-                    path_to_filled = unique_file_path(filled_on_host.replace(host_base,BASE_DIR))
-                    path_to_cleaned_filled = unique_file_path(cleaned_filled_on_host.replace(host_base,BASE_DIR))
+                    path_to_cleaned = unique_file_path(cleaned_on_host.replace(host_base,biomedisa.BASE_DIR))
+                    path_to_filled = unique_file_path(filled_on_host.replace(host_base,biomedisa.BASE_DIR))
+                    path_to_cleaned_filled = unique_file_path(cleaned_filled_on_host.replace(host_base,biomedisa.BASE_DIR))
 
                     # get results
                     subprocess.Popen(['scp', host+':'+cleaned_on_host, path_to_cleaned]).wait()

biomedisa/features/split_volume.py

@@ -0,0 +1,167 @@
+##########################################################################
+##                                                                      ##
+##  Copyright (c) 2019-2024 Philipp Lösel. All rights reserved.         ##
+##                                                                      ##
+##  This file is part of the open source project biomedisa.             ##
+##                                                                      ##
+##  Licensed under the European Union Public Licence (EUPL)             ##
+##  v1.2, or - as soon as they will be approved by the                  ##
+##  European Commission - subsequent versions of the EUPL;              ##
+##                                                                      ##
+##  You may redistribute it and/or modify it under the terms            ##
+##  of the EUPL v1.2. You may not use this work except in               ##
+##  compliance with this Licence.                                       ##
+##                                                                      ##
+##  You can obtain a copy of the Licence at:                            ##
+##                                                                      ##
+##  https://joinup.ec.europa.eu/page/eupl-text-11-12                    ##
+##                                                                      ##
+##  Unless required by applicable law or agreed to in                   ##
+##  writing, software distributed under the Licence is                  ##
+##  distributed on an "AS IS" basis, WITHOUT WARRANTIES                 ##
+##  OR CONDITIONS OF ANY KIND, either express or implied.               ##
+##                                                                      ##
+##  See the Licence for the specific language governing                 ##
+##  permissions and limitations under the Licence.                      ##
+##                                                                      ##
+##########################################################################
+
+import os
+from biomedisa.features.biomedisa_helper import load_data, save_data
+from biomedisa.features.interpolation import smart_interpolation
+from tifffile import imread, imwrite, TiffFile
+import numpy as np
+import argparse
+
+if __name__ == '__main__':
+
+    # initialize arguments
+    parser = argparse.ArgumentParser(description='Biomedisa interpolation.',
+             formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+    # required arguments
+    parser.add_argument('path_to_data', type=str, metavar='PATH_TO_IMAGE',
+                        help='Location of image data')
+    parser.add_argument('path_to_labels', type=str, metavar='PATH_TO_LABELS',
+                        help='Location of label data')
+
+    # optional arguments
+    parser.add_argument('-allx', '--allaxis', action='store_true', default=False,
+                        help='If pre-segmentation is not exlusively in xy-plane')
+    parser.add_argument('-u', '--uncertainty', action='store_true', default=False,
+                        help='Return uncertainty of segmentation result')
+    parser.add_argument('-s', '--smooth', nargs='?', type=int, const=100, default=0,
+                        help='Number of smoothing iterations for segmentation result')
+    parser.add_argument('-ol', '--overlap', type=int, default=50,
+                        help='Overlap of sub-blocks')
+    parser.add_argument('-sx','--split_x', type=int, default=1,
+                        help='Number of sub-blocks in x-direction')
+    parser.add_argument('-sy','--split_y', type=int, default=1,
+                        help='Number of sub-blocks in y-direction')
+    parser.add_argument('-sz','--split_z', type=int, default=1,
+                        help='Number of sub-blocks in z-direction')
+    args = parser.parse_args()
+
+    # image size
+    if args.path_to_data[-4:] == '.tif':
+        tif = TiffFile(args.path_to_data)
+        zsh = len(tif.pages)
+        ysh, xsh = tif.pages[0].shape
+    else:
+        print('Warning: This script is optimized for TIFF files. Please consider saving your data in TIFF format.')
+        data, _ = load_data(args.path_to_data)
+        shape = np.array(data.shape).copy()
+        zsh, ysh, xsh = shape
+        del data
+
+    if args.path_to_labels[-4:] != '.tif':
+        print('Warning: This script is optimized for TIFF files. Please consider saving your labels in TIFF format.')
+
+    # split volume
+    sub_size_z = np.ceil(zsh / args.split_z)
+    sub_size_y = np.ceil(ysh / args.split_y)
+    sub_size_x = np.ceil(xsh / args.split_x)
+
+    # allocate memory
+    final = np.zeros((zsh, ysh, xsh), dtype=np.uint8)
+    if args.smooth:
+        final_smooth = np.zeros_like(final)
+    if args.uncertainty:
+        final_uncertainty = np.zeros_like(final)
+
+    # iterate over subvolumes
+    for z_i in range(args.split_z):
+        for y_i in range(args.split_y):
+            for x_i in range(args.split_x):
+                subvolume = z_i * args.split_y * args.split_x + y_i * args.split_x + x_i + 1
+                print('Subvolume:', subvolume, '/', args.split_z * args.split_y * args.split_x)
+
+                # determine z subvolume
+                blockmin_z = int(z_i * sub_size_z)
+                blockmax_z = int((z_i+1) * sub_size_z)
+                datamin_z = max(blockmin_z - args.overlap, 0)
+                datamax_z = min(blockmax_z + args.overlap, zsh)
+
+                # determine y subvolume
+                blockmin_y = int(y_i * sub_size_y)
+                blockmax_y = int((y_i+1) * sub_size_y)
+                datamin_y = max(blockmin_y - args.overlap, 0)
+                datamax_y = min(blockmax_y + args.overlap, ysh)
+
+                # determine x subvolume
+                blockmin_x = int(x_i * sub_size_x)
+                blockmax_x = int((x_i+1) * sub_size_x)
+                datamin_x = max(blockmin_x - args.overlap, 0)
+                datamax_x = min(blockmax_x + args.overlap, xsh)
+
+                # extract image subvolume
+                if args.path_to_data[-4:] == '.tif':
+                    data = imread(args.path_to_data, key=range(datamin_z,datamax_z))
+                    data = data[:,datamin_y:datamax_y,datamin_x:datamax_x].copy()
+                else:
+                    data, _ = load_data(args.path_to_data)
+                    data = data[datamin_z:datamax_z,datamin_y:datamax_y,datamin_x:datamax_x].copy()
+
+                # extract label subvolume
+                if args.path_to_labels[-4:] == '.tif':
+                    header, final_image_type = None, '.tif'
+                    labelData = imread(args.path_to_labels, key=range(datamin_z,datamax_z))
+                    labelData = labelData[:,datamin_y:datamax_y,datamin_x:datamax_x].copy()
+                else:
+                    labelData, header, final_image_type = load_data(args.path_to_labels, return_extension=True)
+                    labelData = labelData[datamin_z:datamax_z,datamin_y:datamax_y,datamin_x:datamax_x].copy()
+
+                # interpolation
+                results = smart_interpolation(data, labelData, uncertainty=args.uncertainty, allaxis=args.allaxis, smooth=args.smooth)
+
+                # append results
+                final[blockmin_z:blockmax_z,blockmin_y:blockmax_y,blockmin_x:blockmax_x] \
+                    = results['regular'][blockmin_z-datamin_z:blockmax_z-datamin_z,blockmin_y-datamin_y:blockmax_y-datamin_y,blockmin_x-datamin_x:blockmax_x-datamin_x]
+                if 'smooth' in results and results['smooth'] is not None:
+                    final_smooth[blockmin_z:blockmax_z,blockmin_y:blockmax_y,blockmin_x:blockmax_x] \
+                        = results['smooth'][blockmin_z-datamin_z:blockmax_z-datamin_z,blockmin_y-datamin_y:blockmax_y-datamin_y,blockmin_x-datamin_x:blockmax_x-datamin_x]
+                if 'uncertainty' in results and results['uncertainty'] is not None:
+                    final_uncertainty[blockmin_z:blockmax_z,blockmin_y:blockmax_y,blockmin_x:blockmax_x] \
+                        = results['uncertainty'][blockmin_z-datamin_z:blockmax_z-datamin_z,blockmin_y-datamin_y:blockmax_y-datamin_y,blockmin_x-datamin_x:blockmax_x-datamin_x]
+
+    # path to regular result
+    filename, extension = os.path.splitext(os.path.basename(args.path_to_data))
+    if extension == '.gz':
+        filename = filename[:-4]
+    filename = 'final.' + filename
+    path_to_final = args.path_to_data.replace(os.path.basename(args.path_to_data), filename + final_image_type)
+
+    # path to optional results
+    filename, extension = os.path.splitext(path_to_final)
+    if extension == '.gz':
+        filename = filename[:-4]
+    path_to_smooth = filename + '.smooth' + final_image_type
+    path_to_uq = filename + '.uncertainty.tif'
+
+    # save results
+    save_data(path_to_final, final, header)
+    if args.smooth:
+        save_data(path_to_smooth, final_smooth, header)
+    if args.uncertainty:
+        imwrite(path_to_uq, final_uncertainty)
+

biomedisa/interpolation.py

@@ -1,7 +1,7 @@
 #!/usr/bin/python3
 ##########################################################################
 ##                                                                      ##
-##  Copyright (c) 2024 Philipp Lösel. All rights reserved.              ##
+##  Copyright (c) 2019-2024 Philipp Lösel. All rights reserved.         ##
 ##                                                                      ##
 ##  This file is part of the open source project biomedisa.             ##
 ##                                                                      ##
@@ -27,11 +27,9 @@
 ##                                                                      ##
 ##########################################################################
 
-import sys, os
-BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
-sys.path.append(BASE_DIR)
+import os
 import biomedisa
-from biomedisa_features.biomedisa_helper import (_get_platform, smooth_img_3x3,
+from biomedisa.features.biomedisa_helper import (_get_platform, smooth_img_3x3,
     pre_processing, _error_, read_labeled_slices, read_labeled_slices_allx,
     read_indices_allx, predict_blocksize)
 from multiprocessing import freeze_support
@@ -88,14 +86,14 @@ def smart_interpolation(data, labelData, nbrw=10, sorw=4000, acwe=False, acwe_al
 
         # set pid and write in logfile
         if bm.django_env:
-            from biomedisa_features.django_env import create_pid_object
+            from biomedisa.features.django_env import create_pid_object
             create_pid_object(os.getpid(), bm.remote, bm.queue, bm.img_id)
 
             # write in logfile
             bm.username = os.path.basename(os.path.dirname(bm.path_to_data))
             bm.shortfilename = os.path.basename(bm.path_to_data)
-            bm.path_to_logfile = BASE_DIR + '/log/logfile.txt'
-            bm.path_to_time = BASE_DIR + '/log/time.txt'
+            bm.path_to_logfile = biomedisa.BASE_DIR + '/log/logfile.txt'
+            bm.path_to_time = biomedisa.BASE_DIR + '/log/time.txt'
             with open(bm.path_to_logfile, 'a') as logfile:
                 print('%s %s %s %s' %(time.ctime(), bm.username, bm.shortfilename, 'Process was started.'), file=logfile)
 
@@ -256,7 +254,7 @@ def smart_interpolation(data, labelData, nbrw=10, sorw=4000, acwe=False, acwe_al
                     # create subcommunicator
                     sub_comm = MPI.Comm.Split(comm, 1, rank)
 
-                    from biomedisa_features.random_walk.rw_small import _diffusion_child
+                    from biomedisa.features.random_walk.rw_small import _diffusion_child
                     results = _diffusion_child(sub_comm, bm)
 
                 else:
@@ -276,7 +274,7 @@ def smart_interpolation(data, labelData, nbrw=10, sorw=4000, acwe=False, acwe_al
                     # create subcommunicator
                     sub_comm = MPI.Comm.Split(comm, 1, rank)
 
-                    from biomedisa_features.random_walk.rw_large import _diffusion_child
+                    from biomedisa.features.random_walk.rw_large import _diffusion_child
                     results = _diffusion_child(sub_comm, bm)
 
                 return results
@@ -301,10 +299,10 @@ def smart_interpolation(data, labelData, nbrw=10, sorw=4000, acwe=False, acwe_al
                 sub_comm = MPI.Comm.Split(comm, 1, rank)
 
                 if small:
-                    from biomedisa_features.random_walk.rw_small import _diffusion_child
+                    from biomedisa.features.random_walk.rw_small import _diffusion_child
                     _diffusion_child(sub_comm)
                 else:
-                    from biomedisa_features.random_walk.rw_large import _diffusion_child
+                    from biomedisa.features.random_walk.rw_large import _diffusion_child
                     _diffusion_child(sub_comm)
 
 if __name__ == '__main__':

biomedisa/mesh.py

@@ -1,7 +1,7 @@
 #!/usr/bin/python3
 ##########################################################################
 ##                                                                      ##
-##  Copyright (c) 2024 Philipp Lösel. All rights reserved.              ##
+##  Copyright (c) 2019-2024 Philipp Lösel. All rights reserved.         ##
 ##                                                                      ##
 ##  This file is part of the open source project biomedisa.             ##
 ##                                                                      ##
@@ -27,13 +27,10 @@
 ##                                                                      ##
 ##########################################################################
 
-import os, sys
-BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
-if not BASE_DIR in sys.path:
-    sys.path.append(BASE_DIR)
+import os
 import numpy as np
-from biomedisa_features.biomedisa_helper import load_data, unique_file_path
-from biomedisa_features.django_env import create_pid_object
+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
 from stl import mesh
 import vtk
@@ -228,7 +225,7 @@ def init_create_mesh(id):
 
     # get host information
     host = ''
-    host_base = BASE_DIR
+    host_base = biomedisa.BASE_DIR
     subhost, qsub_pid = None, None
     if 'REMOTE_QUEUE_HOST' in config:
         host = config['REMOTE_QUEUE_HOST']
@@ -261,14 +258,14 @@ def init_create_mesh(id):
             if host:
 
                 # command
-                cmd = ['python3', host_base+'/biomedisa_features/create_mesh.py', img.pic.path.replace(BASE_DIR,host_base)]
+                cmd = ['python3', host_base+'/biomedisa/mesh.py', img.pic.path.replace(biomedisa.BASE_DIR,host_base)]
                 cmd += [f'-iid={img.id}', '-r']
 
                 # create user directory
                 subprocess.Popen(['ssh', host, 'mkdir', '-p', host_base+'/private_storage/images/'+img.user.username]).wait()
 
                 # send data to host
-                success = send_data_to_host(img.pic.path, host+':'+img.pic.path.replace(BASE_DIR,host_base))
+                success = send_data_to_host(img.pic.path, host+':'+img.pic.path.replace(biomedisa.BASE_DIR,host_base))
 
                 # qsub start
                 if 'REMOTE_QUEUE_QSUB' in config and config['REMOTE_QUEUE_QSUB']:
@@ -291,14 +288,14 @@ def init_create_mesh(id):
                     subprocess.Popen(cmd).wait()
 
                     # check if aborted
-                    success = subprocess.Popen(['scp', host+':'+host_base+f'/log/pid_7', BASE_DIR+f'/log/pid_7']).wait()
+                    success = subprocess.Popen(['scp', host+':'+host_base+f'/log/pid_7', biomedisa.BASE_DIR+f'/log/pid_7']).wait()
 
                     # get result
                     if success==0:
                         # remove pid file
                         subprocess.Popen(['ssh', host, 'rm', host_base+f'/log/pid_7']).wait()
 
-                        result_on_host = img.pic.path.replace(BASE_DIR,host_base)
+                        result_on_host = img.pic.path.replace(biomedisa.BASE_DIR,host_base)
                         result_on_host = result_on_host.replace(os.path.splitext(result_on_host)[1],'.stl')
                         success = subprocess.Popen(['scp', host+':'+result_on_host, path_to_result]).wait()
 

{biomedisa-2024.5.19.dist-info → biomedisa-2024.5.20.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biomedisa
-Version: 2024.5.19
+Version: 2024.5.20
 Summary: Segmentation of 3D volumetric image data
 Author: Philipp Lösel
 Author-email: philipp.loesel@anu.edu.au
@@ -14,7 +14,7 @@ Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 
-[![biomedisa](biomedisa_app/static/biomedisa_logo.svg)](https://biomedisa.info)
+[![biomedisa](https://raw.githubusercontent.com/biomedisa/biomedisa/master/biomedisa_app/static/biomedisa_logo.svg)](https://biomedisa.info)
 -----------
 - [Overview](#overview)
 - [Hardware Requirements](#hardware-requirements)
@@ -55,7 +55,7 @@ Biomedisa (https://biomedisa.info) is a free and easy-to-use open-source applica
 
 #### Python example
 ```python
-from biomedisa.biomedisa_features.biomedisa_helper import load_data, save_data
+from biomedisa.features.biomedisa_helper import load_data, save_data
 from biomedisa.interpolation import smart_interpolation
 
 # load data
@@ -84,7 +84,7 @@ python -m biomedisa.interpolation C:\Users\%USERNAME%\Downloads\tumor.tif C:\Use
 
 #### Python example (training)
 ```python
-from biomedisa.biomedisa_features.biomedisa_helper import load_data
+from biomedisa.features.biomedisa_helper import load_data
 from biomedisa.deeplearning import deep_learning
 
 # load image data
@@ -124,7 +124,7 @@ If running into ResourceExhaustedError due to out of memory (OOM), try to use sm
 
 #### Python example (prediction)
 ```python
-from biomedisa.biomedisa_features.biomedisa_helper import load_data, save_data
+from biomedisa.features.biomedisa_helper import load_data, save_data
 from biomedisa.deeplearning import deep_learning
 
 # load data
@@ -147,7 +147,7 @@ python -m biomedisa.deeplearning C:\Users\%USERNAME%\Downloads\testing_axial_cro
 
 #### Load and save data (such as Amira Mesh, TIFF, NRRD, NIfTI or DICOM)
 ```python
-from biomedisa.biomedisa_features.biomedisa_helper import load_data, save_data
+from biomedisa.features.biomedisa_helper import load_data, save_data
 
 # load data as numpy array
 # for DICOM, PNG files, or similar formats, 'path_to_data' must reference
@@ -160,7 +160,7 @@ save_data(path_to_data, data, header)
 
 #### Create STL mesh from segmentation (label values are saved as attributes)
 ```python
-from biomedisa.biomedisa_features.biomedisa_helper import load_data, save_data
+from biomedisa.features.biomedisa_helper import load_data, save_data
 from biomedisa.mesh import get_voxel_spacing, save_mesh
 
 # load segmentation
@@ -193,7 +193,7 @@ python -m biomedisa.mesh <path_to_data>
 
 #### Resize data
 ```python
-from biomedisa.biomedisa_features.biomedisa_helper import img_resize
+from biomedisa.features.biomedisa_helper import img_resize
 
 # resize image data
 zsh, ysh, xsh = data.shape
@@ -206,7 +206,7 @@ label_data = img_resize(label_data, new_zsh, new_ysh, new_xsh, labels=True)
 
 #### Remove outliers and fill holes
 ```python
-from biomedisa.biomedisa_features.biomedisa_helper import clean, fill
+from biomedisa.features.biomedisa_helper import clean, fill
 
 # delete outliers smaller than 90% of the segment
 label_data = clean(label_data, 0.9)
@@ -217,7 +217,7 @@ label_data = fill(label_data, 0.9)
 
 #### Accuracy assessment
 ```python
-from biomedisa.biomedisa_features.biomedisa_helper import Dice_score, ASSD
+from biomedisa.features.biomedisa_helper import Dice_score, ASSD
 dice = Dice_score(ground_truth, result)
 assd = ASSD(ground_truth, result)
 ```