biomedisa 2024.5.19__tar.gz → 2024.5.20__tar.gz

{biomedisa-2024.5.19 → biomedisa-2024.5.20}/PKG-INFO

@@ -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)
 ```

{biomedisa-2024.5.19 → biomedisa-2024.5.20}/README.md

@@ -1,4 +1,4 @@
-[![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)
@@ -39,7 +39,7 @@ 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
@@ -68,7 +68,7 @@ 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
@@ -108,7 +108,7 @@ 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
@@ -131,7 +131,7 @@ 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
@@ -144,7 +144,7 @@ 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
@@ -177,7 +177,7 @@ 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
@@ -190,7 +190,7 @@ 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)
@@ -201,7 +201,7 @@ 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)
 ```

{biomedisa-2024.5.19 → biomedisa-2024.5.20}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "biomedisa"
-version = "2024.5.19"
+version = "2024.5.20"
 authors = [
   { name="Philipp Lösel"}, {email="philipp.loesel@anu.edu.au" },
 ]

{biomedisa-2024.5.19 → biomedisa-2024.5.20}/src/biomedisa/__init__.py

@@ -1,15 +1,11 @@
 import os
-import sys
 import subprocess
 
 # from source base directory
 BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
 
-# pip base directory
-if not os.path.exists(os.path.join(BASE_DIR,'biomedisa_features')):
-    BASE_DIR = os.path.dirname(os.path.abspath(__file__))
-    # add BASE_DIR to PYTHONPATH for absolute imports
-    sys.path.append(BASE_DIR)
+# pip installation
+if not os.path.exists(os.path.join(BASE_DIR,'biomedisa/settings.py')):
 
     # metadata
     import importlib_metadata

{biomedisa-2024.5.19 → biomedisa-2024.5.20}/src/biomedisa/deeplearning.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 +27,11 @@
 ##                                                                      ##
 ##########################################################################
 
-import sys, os
-BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
-sys.path.append(BASE_DIR)
+import os
 import biomedisa
-import biomedisa_features.crop_helper as ch
-from biomedisa_features.keras_helper import *
-from biomedisa_features.biomedisa_helper import _error_, unique_file_path
+import biomedisa.features.crop_helper as ch
+from biomedisa.features.keras_helper import *
+from biomedisa.features.biomedisa_helper import _error_, unique_file_path
 from tensorflow.python.framework.errors_impl import ResourceExhaustedError
 import tensorflow as tf
 import numpy as np
@@ -121,7 +119,7 @@ def deep_learning(img_data, label_data=None, val_img_data=None, val_label_data=N
             project = os.path.splitext(bm.shortfilename)[0]
 
             # path to model
-            bm.path_to_model = BASE_DIR + f'/private_storage/images/{bm.username}/{project}.h5'
+            bm.path_to_model = biomedisa.BASE_DIR + f'/private_storage/images/{bm.username}/{project}.h5'
             if not bm.remote:
                 bm.path_to_model = unique_file_path(bm.path_to_model)
 
@@ -129,7 +127,7 @@ def deep_learning(img_data, label_data=None, val_img_data=None, val_label_data=N
             project = os.path.splitext(os.path.basename(bm.path_to_model))[0]
 
         # create pid object
-        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, (bm.path_to_model if bm.train else ''))
 
         # write in log file
@@ -319,7 +317,7 @@ def deep_learning(img_data, label_data=None, val_img_data=None, val_label_data=N
     # django environment
     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
         validation=True if bm.validation_split or (bm.val_images is not None and bm.val_images[0] is not None) else False
         post_processing(bm.path_to_final, time_str, config['SERVER_ALIAS'], bm.remote, bm.queue,
             img_id=bm.img_id, label_id=bm.label_id, path_to_model=bm.path_to_model,
@@ -327,7 +325,7 @@ def deep_learning(img_data, label_data=None, val_img_data=None, val_label_data=N
             train=bm.train, predict=bm.predict, validation=validation)
 
         # write in log file
-        path_to_time = BASE_DIR + '/log/time.txt'
+        path_to_time = biomedisa.BASE_DIR + '/log/time.txt'
         with open(path_to_time, 'a') as timefile:
             if predict:
                 message = 'Successfully segmented ' + bm.shortfilename
@@ -490,7 +488,7 @@ if __name__ == '__main__':
             reference_image_path = bm.path_to_images
         bm.username = os.path.basename(os.path.dirname(reference_image_path))
         bm.shortfilename = os.path.basename(reference_image_path)
-        bm.path_to_logfile = BASE_DIR + '/log/logfile.txt'
+        bm.path_to_logfile = biomedisa.BASE_DIR + '/log/logfile.txt'
     else:
         bm.django_env = False
 

{biomedisa-2024.5.19/src/biomedisa/biomedisa_features → biomedisa-2024.5.20/src/biomedisa/features}/DataGenerator.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-2024.5.19/src/biomedisa/biomedisa_features → biomedisa-2024.5.20/src/biomedisa/features}/DataGeneratorCrop.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-2024.5.19/src/biomedisa/biomedisa_features → biomedisa-2024.5.20/src/biomedisa/features}/PredictDataGenerator.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-2024.5.19/src/biomedisa/biomedisa_features → biomedisa-2024.5.20/src/biomedisa/features}/PredictDataGeneratorCrop.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.             ##
 ##                                                                      ##

{biomedisa-2024.5.19/src/biomedisa/biomedisa_features → biomedisa-2024.5.20/src/biomedisa/features}/active_contour.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 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.curvop_numba import curvop, evolution
-from biomedisa_features.biomedisa_helper import (unique_file_path, load_data, save_data,
+from biomedisa.features.curvop_numba import curvop, evolution
+from biomedisa.features.biomedisa_helper import (unique_file_path, load_data, save_data,
     pre_processing, img_to_uint8, silent_remove)
 import numpy as np
 import numba
@@ -143,7 +140,7 @@ def activeContour(data, labelData, alpha=1.0, smooth=1, steps=3,
     if bm.django_env:
         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_logfile = biomedisa.BASE_DIR + '/log/logfile.txt'
 
     # pre-processing
     bm = pre_processing(bm)
@@ -234,13 +231,13 @@ def refinement(bm):
 
 def post_processing(path_to_acwe, image_id=None, friend_id=None, simple=False, remote=False):
     if remote:
-        with open(BASE_DIR + '/log/config_4', 'w') as configfile:
+        with open(biomedisa.BASE_DIR + '/log/config_4', 'w') as configfile:
             print(path_to_acwe, 'phantom', 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
 
@@ -300,7 +297,7 @@ def init_active_contour(image_id, friend_id, label_id, simple=False):
 
     # 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']
@@ -313,8 +310,8 @@ def init_active_contour(image_id, friend_id, label_id, simple=False):
         if host:
 
             # command
-            cmd = ['python3', host_base+'/biomedisa_features/active_contour.py']
-            cmd += [image.pic.path.replace(BASE_DIR,host_base), friend.pic.path.replace(BASE_DIR,host_base)]
+            cmd = ['python3', host_base+'/biomedisa/features/active_contour.py']
+            cmd += [image.pic.path.replace(biomedisa.BASE_DIR,host_base), friend.pic.path.replace(biomedisa.BASE_DIR,host_base)]
             cmd += [f'-iid={image.id}', f'-fid={friend.id}', '-r']
 
             # command (append only on demand)
@@ -338,8 +335,8 @@ def init_active_contour(image_id, friend_id, label_id, simple=False):
 
             # send data to host
             success=0
-            success+=send_data_to_host(image.pic.path, host+':'+image.pic.path.replace(BASE_DIR,host_base))
-            success+=send_data_to_host(friend.pic.path, host+':'+friend.pic.path.replace(BASE_DIR,host_base))
+            success+=send_data_to_host(image.pic.path, host+':'+image.pic.path.replace(biomedisa.BASE_DIR,host_base))
+            success+=send_data_to_host(friend.pic.path, host+':'+friend.pic.path.replace(biomedisa.BASE_DIR,host_base))
 
             if success==0:
 
@@ -355,14 +352,14 @@ def init_active_contour(image_id, friend_id, label_id, simple=False):
                 subprocess.Popen(cmd).wait()
 
                 # config
-                success = subprocess.Popen(['scp', host+':'+host_base+'/log/config_4', BASE_DIR+'/log/config_4']).wait()
+                success = subprocess.Popen(['scp', host+':'+host_base+'/log/config_4', biomedisa.BASE_DIR+'/log/config_4']).wait()
 
                 if success==0:
-                    with open(BASE_DIR + '/log/config_4', 'r') as configfile:
+                    with open(biomedisa.BASE_DIR + '/log/config_4', 'r') as configfile:
                         acwe_on_host, _ = configfile.read().split()
 
                     # local file names
-                    path_to_acwe = unique_file_path(acwe_on_host.replace(host_base,BASE_DIR))
+                    path_to_acwe = unique_file_path(acwe_on_host.replace(host_base,biomedisa.BASE_DIR))
 
                     # get results
                     subprocess.Popen(['scp', host+':'+acwe_on_host, path_to_acwe]).wait()

{biomedisa-2024.5.19/src/biomedisa/biomedisa_features → biomedisa-2024.5.20/src/biomedisa/features}/assd.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-2024.5.19/src/biomedisa/biomedisa_features → biomedisa-2024.5.20/src/biomedisa/features}/biomedisa_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.             ##
 ##                                                                      ##
@@ -27,9 +27,9 @@
 ##########################################################################
 
 import os
-BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
-from biomedisa_features.amira_to_np.amira_helper import amira_to_np, np_to_amira
-from biomedisa_features.nc_reader import nc_to_np, np_to_nc
+import biomedisa
+from biomedisa.features.amira_to_np.amira_helper import amira_to_np, np_to_amira
+from biomedisa.features.nc_reader import nc_to_np, np_to_nc
 from tifffile import imread, imwrite
 from medpy.io import load, save
 import SimpleITK as sitk
@@ -53,7 +53,7 @@ def silent_remove(filename):
         pass
 
 # create a unique filename
-def unique_file_path(path, dir_path=BASE_DIR+'/private_storage/'):
+def unique_file_path(path, dir_path=biomedisa.BASE_DIR+'/private_storage/'):
 
     # get extension
     username = os.path.basename(os.path.dirname(path))
@@ -116,7 +116,7 @@ def Dice_score(ground_truth, result, average_dice=False):
 
 def ASSD(ground_truth, result):
     try:
-        from biomedisa_features.assd import ASSD_one_label
+        from biomedisa.features.assd import ASSD_one_label
         number_of_elements = 0
         distances = 0
         hausdorff = 0
@@ -389,7 +389,7 @@ def load_data(path_to_data, process='None', return_extension=False):
 
 def _error_(bm, message):
     if bm.django_env:
-        from biomedisa_features.django_env import create_error_object
+        from biomedisa.features.django_env import create_error_object
         create_error_object(message, bm.remote, bm.queue, bm.img_id)
         with open(bm.path_to_logfile, 'a') as logfile:
             print('%s %s %s %s' %(time.ctime(), bm.username, bm.shortfilename, message), file=logfile)

{biomedisa-2024.5.19/src/biomedisa/biomedisa_features → biomedisa-2024.5.20/src/biomedisa/features}/create_slices.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.             ##
 ##                                                                      ##
@@ -28,9 +28,7 @@
 ##########################################################################
 
 import sys, os
-BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
-sys.path.append(BASE_DIR)
-from biomedisa_features.biomedisa_helper import load_data, color_to_gray, img_to_uint8, img_resize, id_generator
+from biomedisa.features.biomedisa_helper import load_data, color_to_gray, img_to_uint8, img_resize, id_generator
 from PIL import Image
 import numpy as np
 from glob import glob

{biomedisa-2024.5.19/src/biomedisa/biomedisa_features → biomedisa-2024.5.20/src/biomedisa/features}/crop_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.             ##
 ##                                                                      ##
@@ -27,16 +27,16 @@
 ##########################################################################
 
 import os
-from biomedisa_features.keras_helper import read_img_list
-from biomedisa_features.biomedisa_helper import img_resize, load_data, save_data, set_labels_to_zero
+from biomedisa.features.keras_helper import read_img_list
+from biomedisa.features.biomedisa_helper import img_resize, load_data, save_data, set_labels_to_zero
 from tensorflow.python.framework.errors_impl import ResourceExhaustedError
 from tensorflow.keras.applications import DenseNet121, densenet
 from tensorflow.keras.optimizers import Adam
 from tensorflow.keras.models import Model, load_model
 from tensorflow.keras.layers import Input, GlobalAveragePooling2D, Dropout, Dense
 from tensorflow.keras.callbacks import Callback, ModelCheckpoint
-from biomedisa_features.DataGeneratorCrop import DataGeneratorCrop
-from biomedisa_features.PredictDataGeneratorCrop import PredictDataGeneratorCrop
+from biomedisa.features.DataGeneratorCrop import DataGeneratorCrop
+from biomedisa.features.PredictDataGeneratorCrop import PredictDataGeneratorCrop
 import tensorflow as tf
 import numpy as np
 from glob import glob

{biomedisa-2024.5.19/src/biomedisa/biomedisa_features → biomedisa-2024.5.20/src/biomedisa/features}/curvop_numba.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-2024.5.19/src/biomedisa/biomedisa_features → biomedisa-2024.5.20/src/biomedisa/features}/django_env.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.             ##
 ##                                                                      ##
@@ -26,15 +26,14 @@
 ##                                                                      ##
 ##########################################################################
 
-import sys, os
-BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
-import subprocess
+import os
+import biomedisa
 
 def create_error_object(message, remote=False, queue=None, img_id=None):
 
     # remote server
     if remote:
-        with open(BASE_DIR + f'/log/error_{queue}', 'w') as errorfile:
+        with open(biomedisa.BASE_DIR + f'/log/error_{queue}', 'w') as errorfile:
             print(message, file=errorfile)
 
     # local server
@@ -57,7 +56,7 @@ def create_pid_object(pid, remote=False, queue=None, img_id=None, path_to_model=
 
     # remote server
     if remote:
-        with open(BASE_DIR + f'/log/pid_{queue}', 'w') as pidfile:
+        with open(biomedisa.BASE_DIR + f'/log/pid_{queue}', 'w') as pidfile:
             print(pid, file=pidfile)
 
     # local server
@@ -74,7 +73,7 @@ def post_processing(path_to_final, time_str, server_name, remote, queue, dice=1.
 
     # remote server
     if remote:
-        with open(BASE_DIR + f'/log/config_{queue}', 'w') as configfile:
+        with open(biomedisa.BASE_DIR + f'/log/config_{queue}', 'w') as configfile:
             print(path_to_final, path_to_uq, path_to_smooth, uncertainty, smooth, str(time_str).replace(' ','-'), server_name, path_to_model, path_to_cropped_image, dice, file=configfile)
 
     # local server
@@ -83,9 +82,9 @@ def post_processing(path_to_final, time_str, server_name, remote, queue, dice=1.
         django.setup()
         from biomedisa_app.models import Upload
         from biomedisa_app.views import send_notification
-        from biomedisa_features.active_contour import init_active_contour
-        from biomedisa_features.remove_outlier import init_remove_outlier
-        from biomedisa_features.create_slices import create_slices
+        from biomedisa.features.active_contour import init_active_contour
+        from biomedisa.features.remove_outlier import init_remove_outlier
+        from biomedisa.features.create_slices import create_slices
         from redis import Redis
         from rq import Queue
 

{biomedisa-2024.5.19/src/biomedisa/biomedisa_features → biomedisa-2024.5.20/src/biomedisa/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

{biomedisa-2024.5.19/src/biomedisa/biomedisa_features → biomedisa-2024.5.20/src/biomedisa/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-2024.5.19/src/biomedisa/biomedisa_features → biomedisa-2024.5.20/src/biomedisa/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}'):