biomedisa 2024.5.18__py3-none-any.whl → 2024.5.20__py3-none-any.whl

biomedisa/{biomedisa_features → features}/keras_helper.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.             ##
 ##                                                                      ##
@@ -27,7 +27,6 @@
 ##########################################################################
 
 import os
-BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
 try:
     from tensorflow.keras.optimizers.legacy import SGD
 except:
@@ -40,12 +39,12 @@ from tensorflow.keras.layers import (
 from tensorflow.keras import backend as K
 from tensorflow.keras.utils import to_categorical
 from tensorflow.keras.callbacks import Callback, ModelCheckpoint, EarlyStopping
-from biomedisa_features.DataGenerator import DataGenerator
-from biomedisa_features.PredictDataGenerator import PredictDataGenerator
-from biomedisa_features.biomedisa_helper import (
+from biomedisa.features.DataGenerator import DataGenerator
+from biomedisa.features.PredictDataGenerator import PredictDataGenerator
+from biomedisa.features.biomedisa_helper import (
     img_resize, load_data, save_data, set_labels_to_zero, id_generator, unique_file_path)
-from biomedisa_features.remove_outlier import clean, fill
-from biomedisa_features.active_contour import activeContour
+from biomedisa.features.remove_outlier import clean, fill
+from biomedisa.features.active_contour import activeContour
 import matplotlib.pyplot as plt
 import SimpleITK as sitk
 import tensorflow as tf
@@ -60,13 +59,11 @@ import re
 import time
 import h5py
 import atexit
-import shutil
+import tempfile
 
 class InputError(Exception):
-    def __init__(self, message=None, img_names=[], label_names=[]):
+    def __init__(self, message=None):
         self.message = message
-        self.img_names = img_names
-        self.label_names = label_names
 
 def save_history(history, path_to_model, val_dice, train_dice):
     # summarize history for accuracy
@@ -307,37 +304,33 @@ def get_labels(arr, allLabels):
         final[arr == k] = allLabels[k]
     return final
 
-def read_img_list(img_list, label_list):
+def read_img_list(img_list, label_list, temp_img_dir, temp_label_dir):
     # read filenames
-    InputError.img_names = []
-    InputError.label_names = []
     img_names, label_names = [], []
     for img_name, label_name in zip(img_list, label_list):
 
         # check for tarball
         img_dir, img_ext = os.path.splitext(img_name)
         if img_ext == '.gz':
-            img_dir, img_ext = os.path.splitext(img_dir)
+            img_ext = os.path.splitext(img_dir)[1]
 
         label_dir, label_ext = os.path.splitext(label_name)
         if label_ext == '.gz':
-            label_dir, label_ext = os.path.splitext(label_dir)
+            label_ext = os.path.splitext(label_dir)[1]
 
         if (img_ext == '.tar' and label_ext == '.tar') or (os.path.isdir(img_name) and os.path.isdir(label_name)):
 
             # extract files
             if img_ext == '.tar':
-                img_dir = BASE_DIR + '/tmp/' + id_generator(40)
                 tar = tarfile.open(img_name)
-                tar.extractall(path=img_dir)
+                tar.extractall(path=temp_img_dir)
                 tar.close()
-                img_name = img_dir
+                img_name = temp_img_dir
             if label_ext == '.tar':
-                label_dir = BASE_DIR + '/tmp/' + id_generator(40)
                 tar = tarfile.open(label_name)
-                tar.extractall(path=label_dir)
+                tar.extractall(path=temp_label_dir)
                 tar.close()
-                label_name = label_dir
+                label_name = temp_label_dir
 
             for data_type in ['.am','.tif','.tiff','.hdr','.mhd','.mha','.nrrd','.nii','.nii.gz','.zip','.mrc']:
                 img_names += [file for file in glob.glob(img_name+'/**/*'+data_type, recursive=True) if not os.path.basename(file).startswith('.')]
@@ -345,15 +338,11 @@ def read_img_list(img_list, label_list):
             img_names = sorted(img_names)
             label_names = sorted(label_names)
             if len(img_names)==0 or len(label_names)==0 or len(img_names)!=len(label_names):
-                if img_ext == '.tar' and os.path.exists(img_name):
-                    shutil.rmtree(img_name)
-                if label_ext == '.tar' and os.path.exists(label_name):
-                    shutil.rmtree(label_name)
                 if len(img_names)!=len(label_names):
                     InputError.message = 'Number of image and label files must be the same'
-                elif img_ext == '.tar':
+                elif img_ext == '.tar' and len(img_names)==0:
                     InputError.message = 'Invalid image TAR file'
-                elif label_ext == '.tar':
+                elif label_ext == '.tar' and len(label_names)==0:
                     InputError.message = 'Invalid label TAR file'
                 elif len(img_names)==0:
                     InputError.message = 'Invalid image data'
@@ -365,165 +354,151 @@ def read_img_list(img_list, label_list):
             label_names.append(label_name)
     return img_names, label_names
 
-def remove_extracted_data(img_list, label_list):
-    for img_name in img_list:
-        if BASE_DIR + '/tmp/' in img_name:
-            img_dir = img_name[:len(BASE_DIR + '/tmp/') + 40]
-            if os.path.exists(img_dir):
-                shutil.rmtree(img_dir)
-    for label_name in label_list:
-        if BASE_DIR + '/tmp/' in label_name:
-            label_dir = label_name[:len(BASE_DIR + '/tmp/') + 40]
-            if os.path.exists(label_dir):
-                shutil.rmtree(label_dir)
-
 def load_training_data(normalize, img_list, label_list, channels, x_scale, y_scale, z_scale, no_scaling,
         crop_data, labels_to_compute, labels_to_remove, img_in=None, label_in=None,
         normalization_parameters=None, allLabels=None, header=None, extension='.tif',
         x_puffer=25, y_puffer=25, z_puffer=25):
 
-    # read image lists
-    if any(img_list):
-        img_names, label_names = read_img_list(img_list, label_list)
-        InputError.img_names = img_names
-        InputError.label_names = label_names
-
-    # load first label
-    if any(img_list):
-        label, header, extension = load_data(label_names[0], 'first_queue', True)
-        if label is None:
-            InputError.message = f'Invalid label data "{os.path.basename(label_names[0])}"'
-            raise InputError()
-    elif type(label_in) is list:
-        label = label_in[0]
-    else:
-        label = label_in
-    label_dim = label.shape
-    label = set_labels_to_zero(label, labels_to_compute, labels_to_remove)
-    label_values, counts = np.unique(label, return_counts=True)
-    print(f'{os.path.basename(label_names[0])}:', 'Labels:', label_values[1:], 'Sizes:', counts[1:])
-    if crop_data:
-        argmin_z,argmax_z,argmin_y,argmax_y,argmin_x,argmax_x = predict_blocksize(label, x_puffer, y_puffer, z_puffer)
-        label = np.copy(label[argmin_z:argmax_z,argmin_y:argmax_y,argmin_x:argmax_x], order='C')
-    if not no_scaling:
-        label = img_resize(label, z_scale, y_scale, x_scale, labels=True)
-
-    # if header is not single data stream Amira Mesh falling back to Multi-TIFF
-    if extension != '.am':
-        if extension != '.tif':
-            print(f'Warning! Please use -hf or --header_file="path_to_training_label{extension}" for prediction to save your result as "{extension}"')
-        extension, header = '.tif', None
-    elif len(header) > 1:
-        print('Warning! Multiple data streams are not supported. Falling back to TIFF.')
-        extension, header = '.tif', None
-    else:
-        header = header[0]
-
-    # load first img
-    if any(img_list):
-        img, _ = load_data(img_names[0], 'first_queue')
-        if img is None:
-            InputError.message = f'Invalid image data "{os.path.basename(img_names[0])}"'
-            raise InputError()
-    elif type(img_in) is list:
-        img = img_in[0]
-    else:
-        img = img_in
-    if label_dim != img.shape:
-        InputError.message = f'Dimensions of "{os.path.basename(img_names[0])}" and "{os.path.basename(label_names[0])}" do not match'
-        raise InputError()
-
-    # ensure images have channels >=1
-    if len(img.shape)==3:
-        z_shape, y_shape, x_shape = img.shape
-        img = img.reshape(z_shape, y_shape, x_shape, 1)
-    if channels is None:
-        channels = img.shape[3]
-    if channels != img.shape[3]:
-        InputError.message = f'Number of channels must be {channels} for "{os.path.basename(img_names[0])}"'
-        raise InputError()
-
-    # crop data
-    if crop_data:
-        img = np.copy(img[argmin_z:argmax_z,argmin_y:argmax_y,argmin_x:argmax_x], order='C')
+    # make temporary directories
+    with tempfile.TemporaryDirectory() as temp_img_dir:
+        with tempfile.TemporaryDirectory() as temp_label_dir:
 
-    # scale/resize image data
-    img = img.astype(np.float32)
-    if not no_scaling:
-        img = img_resize(img, z_scale, y_scale, x_scale)
-
-    # normalize image data
-    for c in range(channels):
-        img[:,:,:,c] -= np.amin(img[:,:,:,c])
-        img[:,:,:,c] /= np.amax(img[:,:,:,c])
-        if normalization_parameters is None:
-            normalization_parameters = np.zeros((2,channels))
-            normalization_parameters[0,c] = np.mean(img[:,:,:,c])
-            normalization_parameters[1,c] = np.std(img[:,:,:,c])
-        elif normalize:
-            mean, std = np.mean(img[:,:,:,c]), np.std(img[:,:,:,c])
-            img[:,:,:,c] = (img[:,:,:,c] - mean) / std
-            img[:,:,:,c] = img[:,:,:,c] * normalization_parameters[1,c] + normalization_parameters[0,c]
-
-    # loop over list of images
-    if any(img_list) or type(img_in) is list:
-        number_of_images = len(img_names) if any(img_list) else len(img_in)
-
-        for k in range(1, number_of_images):
+            # read image lists
+            if any(img_list):
+                img_names, label_names = read_img_list(img_list, label_list, temp_img_dir, temp_label_dir)
 
-            # append label
-            if any(label_list):
-                a, _ = load_data(label_names[k], 'first_queue')
-                if a is None:
-                    InputError.message = f'Invalid label data "{os.path.basename(label_names[k])}"'
+            # load first label
+            if any(img_list):
+                label, header, extension = load_data(label_names[0], 'first_queue', True)
+                if label is None:
+                    InputError.message = f'Invalid label data "{os.path.basename(label_names[0])}"'
                     raise InputError()
+            elif type(label_in) is list:
+                label = label_in[0]
             else:
-                a = label_in[k]
-            label_dim = a.shape
-            a = set_labels_to_zero(a, labels_to_compute, labels_to_remove)
-            label_values, counts = np.unique(a, return_counts=True)
-            print(f'{os.path.basename(label_names[k])}:', 'Labels:', label_values[1:], 'Sizes:', counts[1:])
+                label = label_in
+            label_dim = label.shape
+            label = set_labels_to_zero(label, labels_to_compute, labels_to_remove)
+            label_values, counts = np.unique(label, return_counts=True)
+            print(f'{os.path.basename(label_names[0])}:', 'Labels:', label_values[1:], 'Sizes:', counts[1:])
             if crop_data:
-                argmin_z,argmax_z,argmin_y,argmax_y,argmin_x,argmax_x = predict_blocksize(a, x_puffer, y_puffer, z_puffer)
-                a = np.copy(a[argmin_z:argmax_z,argmin_y:argmax_y,argmin_x:argmax_x], order='C')
+                argmin_z,argmax_z,argmin_y,argmax_y,argmin_x,argmax_x = predict_blocksize(label, x_puffer, y_puffer, z_puffer)
+                label = np.copy(label[argmin_z:argmax_z,argmin_y:argmax_y,argmin_x:argmax_x], order='C')
             if not no_scaling:
-                a = img_resize(a, z_scale, y_scale, x_scale, labels=True)
-            label = np.append(label, a, axis=0)
+                label = img_resize(label, z_scale, y_scale, x_scale, labels=True)
+
+            # if header is not single data stream Amira Mesh falling back to Multi-TIFF
+            if extension != '.am':
+                if extension != '.tif':
+                    print(f'Warning! Please use -hf or --header_file="path_to_training_label{extension}" for prediction to save your result as "{extension}"')
+                extension, header = '.tif', None
+            elif len(header) > 1:
+                print('Warning! Multiple data streams are not supported. Falling back to TIFF.')
+                extension, header = '.tif', None
+            else:
+                header = header[0]
 
-            # append image
+            # load first img
             if any(img_list):
-                a, _ = load_data(img_names[k], 'first_queue')
-                if a is None:
-                    InputError.message = f'Invalid image data "{os.path.basename(img_names[k])}"'
+                img, _ = load_data(img_names[0], 'first_queue')
+                if img is None:
+                    InputError.message = f'Invalid image data "{os.path.basename(img_names[0])}"'
                     raise InputError()
+            elif type(img_in) is list:
+                img = img_in[0]
             else:
-                a = img_in[k]
-            if label_dim != a.shape:
-                InputError.message = f'Dimensions of "{os.path.basename(img_names[k])}" and "{os.path.basename(label_names[k])}" do not match'
+                img = img_in
+            if label_dim != img.shape:
+                InputError.message = f'Dimensions of "{os.path.basename(img_names[0])}" and "{os.path.basename(label_names[0])}" do not match'
                 raise InputError()
-            if len(a.shape)==3:
-                z_shape, y_shape, x_shape = a.shape
-                a = a.reshape(z_shape, y_shape, x_shape, 1)
-            if a.shape[3] != channels:
-                InputError.message = f'Number of channels must be {channels} for "{os.path.basename(img_names[k])}"'
+
+            # ensure images have channels >=1
+            if len(img.shape)==3:
+                z_shape, y_shape, x_shape = img.shape
+                img = img.reshape(z_shape, y_shape, x_shape, 1)
+            if channels is None:
+                channels = img.shape[3]
+            if channels != img.shape[3]:
+                InputError.message = f'Number of channels must be {channels} for "{os.path.basename(img_names[0])}"'
                 raise InputError()
+
+            # crop data
             if crop_data:
-                a = np.copy(a[argmin_z:argmax_z,argmin_y:argmax_y,argmin_x:argmax_x], order='C')
-            a = a.astype(np.float32)
+                img = np.copy(img[argmin_z:argmax_z,argmin_y:argmax_y,argmin_x:argmax_x], order='C')
+
+            # scale/resize image data
+            img = img.astype(np.float32)
             if not no_scaling:
-                a = img_resize(a, z_scale, y_scale, x_scale)
+                img = img_resize(img, z_scale, y_scale, x_scale)
+
+            # normalize image data
             for c in range(channels):
-                a[:,:,:,c] -= np.amin(a[:,:,:,c])
-                a[:,:,:,c] /= np.amax(a[:,:,:,c])
-                if normalize:
-                    mean, std = np.mean(a[:,:,:,c]), np.std(a[:,:,:,c])
-                    a[:,:,:,c] = (a[:,:,:,c] - mean) / std
-                    a[:,:,:,c] = a[:,:,:,c] * normalization_parameters[1,c] + normalization_parameters[0,c]
-            img = np.append(img, a, axis=0)
-
-    # remove extracted data
-    if any(img_list):
-        remove_extracted_data(img_names, label_names)
+                img[:,:,:,c] -= np.amin(img[:,:,:,c])
+                img[:,:,:,c] /= np.amax(img[:,:,:,c])
+                if normalization_parameters is None:
+                    normalization_parameters = np.zeros((2,channels))
+                    normalization_parameters[0,c] = np.mean(img[:,:,:,c])
+                    normalization_parameters[1,c] = np.std(img[:,:,:,c])
+                elif normalize:
+                    mean, std = np.mean(img[:,:,:,c]), np.std(img[:,:,:,c])
+                    img[:,:,:,c] = (img[:,:,:,c] - mean) / std
+                    img[:,:,:,c] = img[:,:,:,c] * normalization_parameters[1,c] + normalization_parameters[0,c]
+
+            # loop over list of images
+            if any(img_list) or type(img_in) is list:
+                number_of_images = len(img_names) if any(img_list) else len(img_in)
+
+                for k in range(1, number_of_images):
+
+                    # append label
+                    if any(label_list):
+                        a, _ = load_data(label_names[k], 'first_queue')
+                        if a is None:
+                            InputError.message = f'Invalid label data "{os.path.basename(label_names[k])}"'
+                            raise InputError()
+                    else:
+                        a = label_in[k]
+                    label_dim = a.shape
+                    a = set_labels_to_zero(a, labels_to_compute, labels_to_remove)
+                    label_values, counts = np.unique(a, return_counts=True)
+                    print(f'{os.path.basename(label_names[k])}:', 'Labels:', label_values[1:], 'Sizes:', counts[1:])
+                    if crop_data:
+                        argmin_z,argmax_z,argmin_y,argmax_y,argmin_x,argmax_x = predict_blocksize(a, x_puffer, y_puffer, z_puffer)
+                        a = np.copy(a[argmin_z:argmax_z,argmin_y:argmax_y,argmin_x:argmax_x], order='C')
+                    if not no_scaling:
+                        a = img_resize(a, z_scale, y_scale, x_scale, labels=True)
+                    label = np.append(label, a, axis=0)
+
+                    # append image
+                    if any(img_list):
+                        a, _ = load_data(img_names[k], 'first_queue')
+                        if a is None:
+                            InputError.message = f'Invalid image data "{os.path.basename(img_names[k])}"'
+                            raise InputError()
+                    else:
+                        a = img_in[k]
+                    if label_dim != a.shape:
+                        InputError.message = f'Dimensions of "{os.path.basename(img_names[k])}" and "{os.path.basename(label_names[k])}" do not match'
+                        raise InputError()
+                    if len(a.shape)==3:
+                        z_shape, y_shape, x_shape = a.shape
+                        a = a.reshape(z_shape, y_shape, x_shape, 1)
+                    if a.shape[3] != channels:
+                        InputError.message = f'Number of channels must be {channels} for "{os.path.basename(img_names[k])}"'
+                        raise InputError()
+                    if crop_data:
+                        a = np.copy(a[argmin_z:argmax_z,argmin_y:argmax_y,argmin_x:argmax_x], order='C')
+                    a = a.astype(np.float32)
+                    if not no_scaling:
+                        a = img_resize(a, z_scale, y_scale, x_scale)
+                    for c in range(channels):
+                        a[:,:,:,c] -= np.amin(a[:,:,:,c])
+                        a[:,:,:,c] /= np.amax(a[:,:,:,c])
+                        if normalize:
+                            mean, std = np.mean(a[:,:,:,c]), np.std(a[:,:,:,c])
+                            a[:,:,:,c] = (a[:,:,:,c] - mean) / std
+                            a[:,:,:,c] = a[:,:,:,c] * normalization_parameters[1,c] + normalization_parameters[0,c]
+                    img = np.append(img, a, axis=0)
 
     # limit intensity range
     img[img<0] = 0
@@ -973,8 +948,6 @@ def load_prediction_data(path_to_img, channels, x_scale, y_scale, z_scale,
     # read image data
     if img is None:
         img, img_header = load_data(path_to_img, 'first_queue')
-        InputError.img_names = [path_to_img]
-        InputError.label_names = []
 
     # verify validity
     if img is None:
@@ -1147,7 +1120,7 @@ def predict_semantic_segmentation(bm, img, path_to_model,
             if extension == '.gz':
                 extension = '.nii.gz'
             bm.path_to_final = os.path.splitext(bm.path_to_final)[0] + extension
-            if bm.django_env and not bm.remote and not bm.tmp_dir:
+            if bm.django_env and not bm.remote and not bm.tarfile:
                 bm.path_to_final = unique_file_path(bm.path_to_final)
 
     # handle amira header

biomedisa/{biomedisa_features → features}/nc_reader.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}/pid.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.             ##
 ##                                                                      ##
@@ -34,7 +34,7 @@ if __name__ == "__main__":
     queue = sys.argv[1]
 
     # path to biomedisa
-    BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+    BASE_DIR = os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
 
     # wait for pid
     while not os.path.exists(BASE_DIR + f'/log/pid_{queue}'):

biomedisa/{biomedisa_features → features}/process_image.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.             ##
 ##                                                                      ##
@@ -27,15 +27,13 @@
 ##                                                                      ##
 ##########################################################################
 
-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 numpy as np
-from biomedisa_features.biomedisa_helper import (load_data, save_data, unique_file_path,
+import os
+import biomedisa
+from biomedisa.features.biomedisa_helper import (load_data, save_data, unique_file_path,
     img_to_uint8, smooth_img_3x3)
-from biomedisa_features.create_slices import create_slices
+from biomedisa.features.create_slices import create_slices
 from shutil import copytree
+import numpy as np
 import argparse
 import traceback
 import subprocess
@@ -61,7 +59,7 @@ def init_process_image(id, process=None):
 
     # 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']
@@ -99,7 +97,7 @@ def init_process_image(id, process=None):
             if host:
 
                 # command
-                cmd = ['python3', host_base+'/biomedisa_features/process_image.py', img.pic.path.replace(BASE_DIR,host_base)]
+                cmd = ['python3', host_base+'/biomedisa/features/process_image.py', img.pic.path.replace(biomedisa.BASE_DIR,host_base)]
                 cmd += [f'-iid={img.id}', '-r']
                 if process == 'convert':
                     cmd += ['-c']
@@ -110,7 +108,7 @@ def init_process_image(id, process=None):
                 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']:
@@ -133,14 +131,14 @@ def init_process_image(id, process=None):
                     subprocess.Popen(cmd).wait()
 
                     # check if aborted
-                    success = subprocess.Popen(['scp', host+':'+host_base+f'/log/pid_5', BASE_DIR+f'/log/pid_5']).wait()
+                    success = subprocess.Popen(['scp', host+':'+host_base+f'/log/pid_5', biomedisa.BASE_DIR+f'/log/pid_5']).wait()
 
                     # get result
                     if success==0:
                         # remove pid file
                         subprocess.Popen(['ssh', host, 'rm', host_base+f'/log/pid_5']).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], suffix)
                         success = subprocess.Popen(['scp', host+':'+result_on_host, path_to_result]).wait()
 
@@ -226,7 +224,7 @@ if __name__ == "__main__":
 
     # set pid
     if bm.remote:
-        from biomedisa_features.django_env import create_pid_object
+        from biomedisa.features.django_env import create_pid_object
         create_pid_object(os.getpid(), True, 5, bm.img_id)
 
     # load data

biomedisa/{biomedisa_features → features}/pycuda_test.py

@@ -1,6 +1,6 @@
 ##########################################################################
 ##                                                                      ##
-##  Copyright (c) 2022 Philipp Lösel. All rights reserved.              ##
+##  Copyright (c) 2019-2024 Philipp Lösel. All rights reserved.         ##
 ##                                                                      ##
 ##  This file is part of the open source project biomedisa.             ##
 ##                                                                      ##
@@ -82,3 +82,4 @@ if __name__ == "__main__":
 
     ctx.pop()
     del ctx
+

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

@@ -1,6 +1,6 @@
 ##########################################################################
 ##                                                                      ##
-##  Copyright (c) 2022 Philipp Lösel. All rights reserved.              ##
+##  Copyright (c) 2019-2024 Philipp Lösel. All rights reserved.         ##
 ##                                                                      ##
 ##  This file is part of the open source project biomedisa.             ##
 ##                                                                      ##
@@ -181,3 +181,4 @@ def _build_curvature_gpu():
     mod = SourceModule(code)
     kernel = mod.get_function("Funktion")
     return kernel
+

biomedisa/{biomedisa_features → features}/random_walk/pycuda_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.             ##
 ##                                                                      ##
@@ -32,7 +32,7 @@ import numpy as np
 import pycuda.driver as cuda
 import pycuda.gpuarray as gpuarray
 from pycuda.compiler import SourceModule
-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_kernel_fill, _build_update_gpu, _build_curvature_gpu)
 
 def reduceBlocksize(slices):

biomedisa/{biomedisa_features → features}/random_walk/pycuda_large_allx.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.             ##
 ##                                                                      ##
@@ -32,7 +32,7 @@ import numpy as np
 import pycuda.driver as cuda
 import pycuda.gpuarray as gpuarray
 from pycuda.compiler import SourceModule
-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_kernel_fill, _build_update_gpu, _build_curvature_gpu)
 
 def reduceBlocksize(slices):

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

@@ -1,6 +1,6 @@
 ##########################################################################
 ##                                                                      ##
-##  Copyright (c) 2023 Philipp Lösel. All rights reserved.              ##
+##  Copyright (c) 20019-2024 Philipp Lösel. All rights reserved.        ##
 ##                                                                      ##
 ##  This file is part of the open source project biomedisa.             ##
 ##                                                                      ##
@@ -30,7 +30,7 @@ import numpy as np
 import pycuda.driver as cuda
 import pycuda.gpuarray as gpuarray
 from pycuda.compiler import SourceModule
-from biomedisa_features.random_walk.gpu_kernels import _build_kernel_fill
+from biomedisa.features.random_walk.gpu_kernels import _build_kernel_fill
 
 def walk(data, slices, indices, indices_child, nbrw, sorw, name, ctx, queue):
 

biomedisa/{biomedisa_features → features}/random_walk/pycuda_small_allx.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.             ##
 ##                                                                      ##
@@ -30,7 +30,7 @@ import numpy as np
 import pycuda.driver as cuda
 import pycuda.gpuarray as gpuarray
 from pycuda.compiler import SourceModule
-from biomedisa_features.random_walk.gpu_kernels import _build_kernel_fill
+from biomedisa.features.random_walk.gpu_kernels import _build_kernel_fill
 import numba
 
 def walk(data, slices, indices_all, indices_child, nbrw, sorw, name, ctx, queue):

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.             ##
 ##                                                                      ##